The asymmetric deformation of silicon wafer alignment mark after lithography process causes an alignment error. Currently, such errors are typically calibrated via process verification; however, this method is challenged by its lack of process adaptability. Herein, we present a new calibration method which uses the differences in alignment positions of the asymmetrically deformed wafer alignment marks under illuminations with different wavelengths and polarizations to calibrate the alignment error, and the proposed method exhibits good process adaptability. Additionally, the proposed calibration method is extended to calibrate the overlay measurement error, improving the process adaptability of overlay measurement.