Perfect Cherry Blossom features three playable characters to choose from, and each character has two different sets of skills. Reimu Hakurei is relatively balanced in all areas. Marisa Kirisame moves faster, and uses more powerful attacks with less range. Sakuya Izayoi moves slower, and uses weaker attacks that can hit just about everything on the screen.

A major addition to Perfect Cherry Blossom is the "Cherry" scoring system. Shooting enemies increases your Cherry Points, bombing or dying decreases your Cherry Points, and reaching 50,000 Cherry Points gives you a temporary shield. Cherry Points eventually lead to a higher Cherry Gauge, which increases the points you receive from Point Items.

Other important changes are the appearance of your character's hitbox while you are focused, the properties of your attacks depending on whether you are focused or unfocused, and a helpful cursor along the bottom margin during a boss battle that shows the location of the boss.

This game is also unique in that it includes a "Phantasm Stage" that can be played only after clearing the Extra Stage. ZUN stated that the Extra Stage in this game was meant to be an "easy mode" version; perhaps Phantasm Stage was the original Extra Stage during development.