The clinical in vivo tissue bulks’ surface is always coarse and shows a complex microscopic geometry which may affect the visual effect of polarization images and calculation of polarization parameters of the sample. To confirm whether this effect would cause identification difficulties and misjudgments on the target recognition when performed the polarization imaging based on 3 × 3 Mueller matrix measurement, cylindrical type and slope type physical models were used to study and analyze the effect of the surface with complex microscopic geometry on the polarization images. Then, clinical tumor bulk samples were used to interact with different sizes of patterns to simulate the different complex microscopic geometry and test the coarse surface effect on polarization images. Meanwhile, assessment parameters were defined to evaluate and confirm the variation between two polarization images quantitatively. The results showed that the polarization imaging of the sample surface with the complex microscopic geometry led to acceptable visual effect and limited quantitative variation on the value of polarization parameters and assessment parameters, and it caused no identification difficulties on target recognition, indicating that it is feasible to apply the polarization imaging based on 3 × 3 Mueller matrix measurement on clinical in vivo tissues with the complex microscopic geometry sample surface.