A method for compensating a design image of a workpiece and a system for processing the design image of the workpiece are disclosed. The method includes the following steps. Obtaining a real image of the workpiece, with the real image having registration holes. Calculating a slope value for each of the registration holes. Determining an amount of interpolation points between each two neighboring registration holes of the registration holes according to the slope value corresponding to each of the registration holes. Obtaining positions of control points in blocks formed by the registration holes. Compensating the design image of the workpiece according to positions of the registration holes, positions of the plurality of interpolation points and the positions of the control points for generating a mapping image. Outputting the mapping image adapted to be mapped onto the workpiece. The system, together with the method, will be introduced.