Stokes ellipsometer can quickly measure polarization state of light beam. Accurate measurement of instrument matrix is one of the most important technology in stokes ellipsometer. In order to improve measurement accuracy of the instrument matrix, a method of multi-point calibration for stokes ellipsometry system is proposed and is proved in theory. Six-point calibration method based on multi-point calibration method is used on the system, which is verified by experiment. Results show that using multi-point calibration method calibration of the system is entirely feasible. It provides a new approach for calibration of Stokes ellipsometer, and six-point calibration method is more accurate than standard of four-point and E-P calibration method in acquiring matrix of the instrument. In measurement accuracy, the total root-mean-square (RMS) deviation of Stokes parameters is 3.15%.