Like the previous high-definition port in the Zelda series (The Legend of Zelda: The Wind Waker HD (2013)), this HD remake was released during the 10-year anniversary of its original, The Legend of Zelda: Twilight Princess (2006).

This is the only Legend of Zelda game in the series to be officially developed for and released separately on three different Nintendo systems (not counting emulated versions of games via Virtual Console). The original versions for the GameCube and Wii were developed and released almost simultaneously in 2006, and the HD remake was released for the Wii U in 2016. While it is true that The Legend of Zelda: Ocarina of Time (1998) was initially released on the Nintendo 64, and subsequently developed as the Master Quest version for the GameCube and a 3D remake for the 3DS, the GameCube version was always part of a collection or included as bonus content, and never sold separately.

The Hero's Shade (the skeletal warrior who teaches Link sword techniques throughout the game) is the Hero of Time from Ocarina of Time and Majora's Mask, who died lamenting he wasn't remembered as a hero, as well as not passing on his skills.

Contrary to the original The Legend of Zelda: Twilight Princess (2006) and The Legend of Zelda: Skyward Sword (2011), this game continues the long series tradition where Link is left-handed. The former games were initially released for the Nintendo Wii console, where Link's sword was controlled by the Wiimote that was typically held in the right hand. So as to not confuse players, Link was made right-handed in those games. In the Wii version of Twilight Princess, everything was mirrored as compared to the GameCube version (i.e. East in the GameCube version was West in the Wii version), so this HD remake is identical to the GameCube version with regards to the world orientation.

The fisherman from Ocarina of Time can be seen in a photo at Hena's Fishing Hole. Hena thinks she is related but she "can't exactly PROVE it." She also scratches like the fisherman, further linking them together.

Twilight Princess is one of the few Zelda games that does not have a magic meter. Originally, the magic meter was planned to be in the game, and can even be seen on one of the screenshots on the back of the box. Unused text left in the game reveals that Link would need magic to transform into his wolf form.

Madame Fanadi, the fortune teller, says strange words while looking into the future. When you reverse her gibberish, you get coherent sentences. If you ask about love she says, "Wait... loading takes awhile." If you ask her about your career she says, "What am I talking about?"

If the player attacks a Cucco enough, they will eventually take control of the Cucco. This breaks the conventions of attacking Cuccos in the Legend of Zelda series, as they would usually flock together and attack the player.

Using the lantern inside of Barnes' Bomb Shop will trigger a cutscene where Barnes will activate a sprinkler to put out the lantern.

Fyer, the man with the cannon at Lake Hylia, has a Bullet Bill from Super Mario Bros. on his sleeve.

The realistic style of Twilight Princess and the return to one giant landmass as the overworld was a direct response to criticism that many players had of the previous game, Legend of Zelda: The Wind Waker (2002), which featured cell-shaded graphics and a giant sea as the overworld. Some of the gameplay elements of Wind Waker had also drawn considerable backlash (most of which were adapted in the HD remake). In spite of the fact that Wind Waker had received excellent reviews, its commercially disappointing results convinced the creative team that for the next installment, they had to give the fans "the Zelda that they wanted". Players in general were much more satisfied with it, because for Twilight Princess' HD remake, very few gameplay changes were implemented.

The Hylian, Goron, Zora and Sheikah races from The Legend of Zelda: Ocarina of Time (1998) all make appearances in this game; missing are the Gerudo warriors (if Ganondorf is disregarded), the Kokiri tribe and the Deku Shrubs. Despite an area called the Gerudo Desert, no Gerudos are found there. It is implied that Telma, the barmaid in Hyrule Castle Town, is of Gerudo descent, given the color of her skin, hair and eyes, as well as a Gerudo symbol she has on her apron. All that remains of the Kokiri tribe is their symbol on the doors in the Forest Temple, implying that they lived there and left or died out. No trace remains of the Deku Shrubs, however.

The melody what Link whistles on Horse Grass to call Epona is the same as 'Epona's Song' from The Legend of Zelda: Ocarina of Time (1998). The theme heard while talking to Rutela, Queen of the Zoras, is the 'Serenade of Water' from the same game.

The ladybugs found in the game have the symbol of the Triforce on their back.

Most of the seven melodies that Link can howl in wolf form are melodies heard in earlier Legend of Zelda games. In the order that they are learned in the game: the 'Song of Healing' from The Legend of Zelda: Majora's Mask (2000); 'Requiem of Spirit' from The Legend of Zelda: Ocarina of Time (1998); 'Prelude of Light' from Ocarina of Time; 'Zelda's Lullaby' from Ocarina of Time; the main title theme from The Legend of Zelda: Oracle of Ages/Oracle of Seasons (2001). The sixth melody is probably an original composition, but the final one is the Twilight Princess theme.

Early designs of Ilia (Link's childhood friend) show her with a symbol on her forehead. The symbol looks like Navi, Link's fairy companion from Zeruda no densetsu: Toki no okarina (1998) (Ocarina of Time), suggesting that there is a link between the two characters. Ilia also has a bow on her back which give the appearance of wings.

The character of Purlo, the man who runs the STAR Game in the big tent in Castle Town, is supposed to be a realistic version of Tingle from The Legend of Zelda: The Wind Waker. Both wear a green vest with a pointy head cover, and they both wear a pocket watch.

In contrast to the original game, in the HD remake, Midna's reflection can be seen in mirrors and ice.

Midna was designed as a Middle-Eastern princess, as a contrast to Zelda, who is a typical European-style princess. Renado and his daughter Luda are reminiscent of Native Americans, which fits with the Western style of their home, Kakariko Village.

It was at one point considered to make Impaz a man, which would have made him the first male Sheik in the series. However, the makers decided to stick with the tradition of making the character a woman.

The Oocca species is based on work of artist Amedeo Modigliani, although some gamers have also seen some similarity with the work of M.C. Escher, whose painting 'Another World' also features bird-like beings walking against walls.

Some of the designs or Darbus, the Goron elder, show him with a white cat on his shoulder. This is the same animal that ended up being Telma's cat, implying that the creature may initially have had a different role in the story.

Telma, the bar maid of Castle Town, and her cat Louise are an obvious nod to Thelma & Louise (1991).

A Zora King was originally meant to appear alongside Queen Rutela. Design sketches show him looking quite similar to King Zora from Legend of Zelda: Ocarina of Time, but in the final game, the king is long dead.

According to the official Legend of Zelda timeline that was created by the makers themselves, the Zelda chronology is split in parallel timelines during The Legend of Zelda: Ocarina of Time (1998). This created a Child Era and an Adult Era timeline. The Legend of Zelda: Twilight Princess (HD) is a sequel to the Child Era of Ocarina of Time, and to The Legend of Zelda: Majora's Mask (2000)..

Midna's voice clips are made up off scrambled pseudo-speech. When unscrambled, it is revealed that she is actually speaking in English.

This game came out the same day the movie "Zootopia" was released.

Ganondorf makes his appearance very late in to the game. He is first mentioned after the fourth dungeon, but we do not see him for the first time until the after the eighth dungeon is completed.

The Fused Shadow from Twilight Princess bears a striking similarity to Majora's Mask. It is highly possible that Majora's Mask was created by the same tribe who made the Fused Shadow, known as the Dark Interlopers. This is made even more probable due to the fact that Twili are seen frequently wearing masks, as Zant and his Guard both wear masks, as well as the Shadow Beasts. In addition, when you steal the Ordon Shield from the village in Twilight Princess, Midna attempts to wear it on her face, like you would a mask.