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.

PROLOGUE

In Gensokyo, people relax and bask in the calm of a winter without end. Spring has shown no sign of arriving even though it's already May, and in fact the snowstorms are continually getting worse. Reimu Hakurei, a shrine maiden of the Hakurei Shrine, is tired of being cold day in and day out and wants to find the source of this unnatural weather. Marisa Kirisame, a black-clothed magician, sees a cherry blossom petal float down outside her warm house and wonders if spring is happening somewhere else. Sakuya Izayoi, the maid leader of the Scarlet Devil Mansion, knows that their winter supplies are diminishing quickly, and wants to end this prolonged winter before they run out completely. Depending on who you choose, only one of these three heroines actually goes out and investigates.

MAIN STORY

The heroine starts off her journey by heading off into the snow-covered forests in search of clues. She battles the ice fairy Cirno and the winter spirit Letty Whiterock in the forest, and the nekomata Chen in the village of Mayohiga, without any progress in her search. Finally, after defeating Alice Margatroid and her dolls, the heroine finds a lead when she notices several cherry blossoms blowing around in the sky. The heroine follows the trail of cherry blossoms high above Gensokyo, breaking through the greetings of Lily White, eventually reaching a great magical boundary and the poltergeist musicians Prismriver Sisters. After silencing the Prismriver Sisters, the heroine crosses the boundary into the Netherworld.