Shining Hearts is a 3D party based role-playing game played from a bird's view perspective. The player can explore various islands in the game, starting with the island of Wyndaria, or use the ship to travel the seas and visit other islands. Player's ship can be upgraded and added various functionality over time. The battle screen is split into a grid formation with front and back row, and the battle itself is turn-based. The player can select physical attack with weapons, use magic, or choose the guard move to boost the defense. The game features typical RPG elements such as trading weapons and items with merchants, performing various mini-game activities, upgrading your characters, solving side quests, and shaping the world in the game based on player's actions.
By performing side quests, player will earn special hearts which will help Kaguya regain her emotions and in turn open gates to new places to progress the main story. Based on player's actions, the hearts that will be collected may change in color and affect the world in that manner. Each color depicting an awarded emotion, such as happiness, kindness, anger, sadness or hatred.