The semi-sequel to the Square-developed Super NES title "Super Mario RPG," Paper Mario's Mushroom Kingdom characters are clearly its only features which are two-dimensional.

A distinguishing characteristic of Paper Mario is that, while the game features a 3D environment similar to that used in Super Mario 64, the characters are designed as flat two-dimensional sprites reminiscent of 16-bit Mario titles, creating the impression of the characters being paper figurines.

Another departure from previous Mario games and from RPGs in general is the game's narration. The story is divided into eight chapters and a prologue. The beginning of a new chapter is announced with a cutscene and a scene with a curtain opening, similar to in a theatrical production. When the chapter is completed, another cutscene is shown with the curtain closing. In between these chapters, interludes showing dialogue between other characters take place, advancing the story. These interludes are also times when the player takes control of Princess Peach and attempts to navigate the castle while avoiding being seen by Bowser's guards.