A method of inspecting a substrate is disclosed. The method is performed by a substrate-inspecting apparatus having at least one projecting module projecting a patterned light onto a substrate fixed on a stage and an inspecting module with a camera capturing an image, and inspecting a plurality of inspection regions of the substrate step by step. The method comprises, setting an inspection order of the inspecting regions according to a lengthwise direction of the substrate, estimating height displacement of a target inspection region by using a tendency information regarding at least one previous inspection region that is already inspected, adjusting height of the inspecting module by using the estimated height displacement of the target inspection region, and inspecting the target inspection region by using the inspecting module of which height is adjusted. Therefore, inspection time is reduced.