A defect inspection and repairing method is disclosed. The method includes: providing a wafer including a semiconductor chip disposed on a surface of the wafer; disposing a layer over the semiconductor chip; obtaining a scanned image of the disposed layer; performing an image analysis upon the scanned image to obtain a defect information; and generating a recipe of a beam according to the defect information, wherein the beam is configured to apply on the disposed layer. Associated system and non-transitory computer-readable medium are also disclosed.