Mueller matrix imaging polarimeter is an effective instrument in measuring the polarization characteristics of materials and devices as well as the polarization aberration of immersion lithography tool, which is composed by polarization state generator and polarization state analyzer. The retardance and fast axis alignmen in the quarter-wave plates and the alignment error in polarizer are the main factors in influencing the measurement accuracy of the Mueller matrix imaging polarimeter. We measure the five primary parameter errors of the Mueller matrix imaging polarimeter of our laboratory developed. The measurement accuracy can be significantly enhanced. The calibration and compensation are carried out by Fourier analysis method. The experiment results show that the measurement accuracy of Mueller matrix imaging polarimeter has been increased from 0.2015 to 0.1051, which is 47.84% better than the un-calibrated one. At last, we measure the polarization aberration of projector with the calibrated Mueller matrix imaging polarimeter. The measurement repeatability is better than 1.1%.