A method for inspecting substrate internal defects is disclosed. The method provides at least one light source disposed on a lateral side of a substrate and configured to emit a light beam to the lateral side for correspondingly penetrating the substrate. The method also provides an image capturing module for retrieving an image of the upper surface, wherein an incident angle of the light beam to the respective lateral side is limited within a first predetermined angle to allow the light beam to have a total reflection in the substrate. Thus, the light beam is blocked by internal defects when transmitting within the substrate to generate bright spots to be detected by the image capturing module for locating the defect position. The method provides a better image definition of internal defects images. The present invention further provides an apparatus based on the method for inspecting substrate internal defects.