A method for defect inspection of a transparent substrate comprises (a) providing an optical system for performing a diffraction process of object wave passing through a transparent substrate, (b) interfering and wavefront recording for the diffracted object wave and a reference wave to reconstruct the defect complex images (including amplitude and phase) of the transparent substrate, (c) characteristics analyzing, features classifying and sieving for the defect complex images of the transparent substrate, and (d) creating defect complex images database based-on the defect complex images for comparison and detection of the defect complex images of the transparent substrate.