The game was originally pitched as a Legend of Zelda game with Link as the protagonist. The game's director, Shinya Hiratake, didn't think it could be a Mario game at first since all of the Mario characters could jump, and he wanted to remove the jumping mechanic.

When presenting the idea of a game featuring Link where the player explores small dioramas to the heads of Nintendo, Miyamoto at first thought they wanted to produce actual dioramas. Though the idea wasn't turned into a full game at first, it was allowed to be incorporated into Super Mario 3D World as a mini-game. Later, Miyamoto encouraged them to take the mini-game and make it into a full game.

The hidden Luigi sprites from New Super Luigi U reappear in this game, as well as a pixelart Rosalina on a book.

In the English version, the 4th section of Chapter 1 is titled: "Onward, Captain Toad!", which is the game's Japanese title.

In Level 1, Episode 16 - Bizarre Doors of Boo Mansion - waiting on the backside of the level for 5 minutes will cause ghostly hand prints to appear on the wall of the mansion.