Compared with conventional microscopy imaging technology, Mueller matrix polarization microscopy imaging can provide more information about a medium’s microstructure characteristics. This paper presents the designs for a set of microscopy imaging systems based on the rotation of dual waveplates that achieve fast Mueller matrix computing-based imaging by selecting special uncorrelated incident polarization states. The system is then employed in imaging studies on onion inner epidermal cells immersed in glucose solutions with different mass fractions and human laryngeal carcinoma cells in different active states. Experimental results show that the measurement error of the system is less than 4.35%. Compared with traditional intensity imaging, which characterizes the surface structure of the sample, polarization imaging can detect changes in the sample more effectively, thereby providing a new research method for the biomedical field.