The game can be optionally played with the stylus, though controls are more simplified compared to Rhythm Heaven.
The game uses the traditional control scheme featured in the original Rhythm Tengoku, which uses the A, B, and directional buttons on the Nintendo 3DS. Like the previous three entries in the series, Rhythm Heaven Megamix is composed of several Rhythm Games, requiring players to play in time with the music in order to clear each one. See also: Gameplay of the Rhythm Heaven series