A system for non-uniformity pattern identification. A storage device stores multiple theoretical patterns and measurements. Each measurement corresponds to a region on a wafer. The processing unit acquires the theoretical patterns and the measurements on at least two wafers, calculates pattern scores for the respective theoretical patterns of each wafer according to the measurements, and groups at least two of the theoretical patterns into at least one factor according to the pattern scores to identify one or more non-uniformity patterns for the wafers. Each pattern score represents the extent of similarity between one of the theoretical patterns and the measurements in one of the wafers.