A method and a system for repairing a defective pixel, and a display panel are provided, the method including: positioning a center of the defective pixel to obtain a center coordinate of the defective pixel; and repairing the defective pixel according to the center coordinate. By the method, the conventional manual alignment operation is replaced with the automatic positioning of the center coordinate, which not only accelerates repairing of the defective pixel, but also improves repairing efficiency, enhances overall efficiency and productivity of the device, and meanwhile, can solve the problem of unsuccessful repairing due to error in manual operation; and the accuracy of the repairing can be improved by automatically positioning the center.