The present invention provides a substrate inspection method for inspecting the substrate is the object to be measured formed by the plurality of projection portions. According to the substrate inspection method of the present invention, by sequentially irradiated with a pattern light on the substrate is the object to be measured is formed to obtain the projection bubyeol phase data for the substrate through the plurality of projection portions. Then, using the projection bubyeol phase data to extract the projection bubyeol height data for the substrate. Then, it is correcting the inclination of the height data extracted by the projection bubyeol height data for each portion of each projection. Then, the tilt and align the projection bubyeol height data a load compensation is completed, extracted the integrated height data using an ordered height data. In this way, by giving compensate the inclination of the height data measured by each unit, each projection before aligning the height of the data extracted from the plurality of the projection portions, it is possible to improve the reliability of the integrated height data.