Mueller matrix microscopy can provide a comprehensive description of sample’s polarization properties non-invasively, and has shown attractive applications in many different fields such as biomedicine, marine particle monitoring, and material identification. Mueller matrix measurements are based on multiple light intensity measurements under illuminations of different polarization states, therefore have more error sources compared to other imaging methods, which reduce the image quality and hinder efforts for quantitatively characterizing the polarization features of weak polarization biological samples such as living cells. Measurement errors of a Mueller matrix microscope are mainly classified into three categories including systematical error, random noise, and mismatch error. In this paper, based on the physical realizability of Mueller matrix and image frequency analysis, different categories and sources of measurement errors in Mueller matrix microscopy are analyzed in detail, a no-reference Mueller matrix image quality evaluator (MIQE) is also proposed to estimate the error level of biomedical sample’s Mueller matrix.