The Stokes vector measurement error equation including alignment errors of half-wave plate (HWP) and quarter-wave plate (QWP) fast axes is established. The influences of alignment errors of wave plate fast axes on Stokes vector measurement accuracy for seven typical incident lights are analyzed. A calibration method of Stokes vector measurement errors for any incident light is given. The simulation results show that the greater the degree of polarization is, the larger the polarization measurement error is. The polarization measurement accuracy is selected to evaluate the system performance when the degree of polarization for the incident light equals to 1. A method for optimizing the alignment errors of wave-plate fast axes is proposed. When the condition number of the measurement matrix is less than 1.84, the selection of splitting ratio 0.772/0.228 can minimize the influences of alignment errors of wave-plate fast axes on the polarization measurement accuracy. To ensure a polarization measurement accuracy of 2%, the alignment error of HWP fast axis should be within ±0.15° and that of QWP fast axis is within ±0.52°.