Due to the sensitivity of wave plates to the angle of incidence (AOI) of light, the accuracy of a dual rotating retarder Mueller matrix polarimeter is also influenced by the AOI. Unlike other conventional systematic errors, the phase retardance error of wave plates caused by AOI is a periodic perturbation rather than a constant. We propose a new method to eliminate the influence of AOI based on a numerical calibration method. To verify the reliability of the proposed calibration method, we measured various types of samples in a transmission Mueller matrix measuring system, such as air, dichroic samples, and birefringent samples, with different AOI conditions. It is demonstrated that the new calibration method can effectively eliminate the influence of AOI. After calibration, the maximum measurement error can be reduced to less than 0.02.