The present invention relates to a method of generating reference data for inspecting a circuit board. The method comprises steps of scanning a bare circuit board to obtain image information of the bare circuit board, generating a compensation matrix using pad coordinate information extracted from the image information and pad coordinate information prestored in design data, and generating, by applying the compensation matrix to the image information, a reference data including coordinate information of a distinctive object. According to the method, inspection efficiency may optimized through quickly generating reference data without CAD information necessary for circuit board inspection.