A defect detecting method, a defect detecting system, and a non-transitory computer-readable medium are provided. The defect detecting method includes applying a rank filter to multiple scan images of consecutive dies of a reference wafer scanned by a wafer inspection tool to obtain multiple reference die images; collecting multiple target die images of a target die of a target wafer scanned by the wafer inspection tool; comparing the target die images with the reference die images to detect multiple defects according to differences of pixel values of corresponding pixels in the target die images and the reference die images; and excluding multiple common defects from the detected defects to detect at least one mask defect printed on the target wafer, where the common defects are obtained by the wafer inspection tool performing a wafer inspection on the target wafer.