This game features two playable characters to choose from, with two different attack types each. Reimu Hakurei can pepper a wide area of the screen with weaker attacks, while Marisa Kirisame relies on her power to compensate for her narrower attack spread. The bombs also exhibit unique behavior and damage amounts depending upon the character chosen.

Lotus Land Story is the first game in the Touhou Project to feature bombs that auto-collect items, graze counting, the ability to move more slowly by holding the shift key, and a non-trivial scoring system that involves the collection of special dream items that boost the player's ultimate scoring potential. The game's scoring system also marks the series' first instance of score bonuses for the elimination of bullets following the defeat of mid-bosses and bosses.