In a method of analyzing a wafer sample, a first defect of a photoresist pattern on the wafer sample having shot regions exposed with related exposure conditions is detected. A first portion of the pattern includes the shot regions exposed with an exposure condition corresponding to a reference exposure condition and a tolerance error range of the reference exposure condition. The first defect repeatedly existing in at least two of the shot regions in a second portion of the pattern is set up as a second defect of the pattern. A first reference image displaying the second defect is obtained. The first defect of the shot regions in the first portion corresponding to the second defect is set up as a third defect corresponding to weak points of the pattern. The exposure conditions of the shot region having no weak points are set up as an exposure margin of an exposure process.