Nanosaur is a third-person action game. The player must find each of the five types of eggs and bring them to time portals. The location of the nearest time portal is always indicated by an onscreen "temporal compass" arrow. The Nanosaur can fly with his jetpack, but the amount of fuel is limited. Pickups with ammunition, health refills, and energy shields can be found strewn about, and fuel can be recharged by standing near gas fissures.

For his defense against the wild dino populace, the Nanosaur is equipped with a "fusion blaster" weapon which has numerous attack modes, each using a different type of ammunition. Apart from the dinosaurs, the player must also watch out for other threats such as lava, rolling boulders, or spore shooting fungi.