Disclosed is a substrate treating apparatus that performs a heat treatment to a substrate. The apparatus includes the following elements: a heat treating plate; a casing that produces a heat treatment atmosphere by the heat treating plate; a movable top board that is movable between a ceiling surface of the casing and the heat treating plate; and a controller that causes the movable top board to be moved to a raised position when the substrate is loaded/unloaded, and causes the movable top board to be moved to a lowered position when the substrate is placed on the heat treating plate for performing the heat treatment, thereby controlling the lowered position for every substrate.