Abstract: Polarization imaging with mueller matrix can be used to obtain the physiological information of superficial biological tissue, which has significant importance in early diagnosis and prevention of cancerous disease. However, the mueller matrix deduced by the polarization information collected from the commercial CMOS sensor directly is not correct, which limits the application of commercial micro CMOS sensor in the endoscopic imaging. The study on commercial area CMOS sensor indicates its non-linear input to output mapping relationship for sensed light intensity. Considering the inherent background noise, a calibration-based method was proposed to mapping the output of the CMOS sensor to obtain the correct polarization information for tested samples. Experiment results demonstrate that the correct mueller matrix can be deduced according to the corrected polarization information, and the error compared to the standard air mueller matrix is below 3%. The effectiveness of this method is demonstrated by the experiment implemented on silk sample. The results of the proposed method reveal the possibility to apply commercial micro CMOS sensor on the endoscopic tip for in vivo biological tissue mueller matrix measurement.