Methods and systems for diagnosing a semiconductor wafer are provided. A plurality of raw images of the semiconductor wafer are obtained according to GDS information regarding a layout of a target die, by an inspection apparatus. A first image-based comparison is performed on the raw images, so as to provide a comparison result, by a determining circuitry. The comparison result indicates whether an image difference is present between the images. One of the raw images having the image difference is assigned as a defect image. A second image-based comparison is performed on a reference image and the defect image, so as to classify a defect type of the image difference, by the determining circuitry. The layout of the target die includes a circuit with a duplicate layout formed by a plurality of same cells. The number of the plurality of raw images is greater than 2.