A substrate inspection apparatus according to an embodiment of the present invention comprises a projection unit, an illumination unit, an image acquisition unit and a processing unit. The projection unit irradiates an inspection target with light for obtaining three-dimensional shape information of the inspection target. The illumination unit irradiates the inspection target with at least two lights having different colors. The image acquisition unit acquires a first image by receiving light irradiated by the projection unit and reflected from the inspection target, and a second image by receiving the lights irradiated by the illumination unit and reflected from the inspection target. The processing unit acquires brightness information and color information from the first image and the second image, respectively, which are acquired by the image acquisition unit, and acquires at least a portion of a boundary by using the bright information and the color information. Therefore, the accuracy and reliability of the inspection can be improved.