Skyward Sword is an action-adventure game with role-playing and puzzle elements. The player controls the protagonist Link from a third-person perspective in a three-dimensional space. Link primarily engages in combat with enemies using a sword and shield, but many other weapons, such as a bow and arrow and bombs, become available as the player progresses. Link also obtains a series of new items, such as a whip and a mechanical flying beetle, that allow him to reach previously inaccessible areas.

Link's adventures consist of traveling between Skyloft, a community based on floating islands in the sky that act as the game's main hub, and Hyrule, which is located directly below on the Earth. Skyloft contains a bazaar where the player can purchase or upgrade potions, shields, and weapons. Initially, access to Hyrule is sealed off by a "cloud barrier," but portals through the clouds to each of the three provinces of Hyrule (forest, volcano, and desert) open as the game progresses.