In a laser transmission system that uses an adaptive optical system, the polarization effect of optical thin films will cause the polarization chromatic aberration, decreasing the correction ability of the system. In this study, the polarization chromatic aberration analysis of the Cassegrain system is performed. First, we employ the Jones Matrix to describe the impact of the polarization aberration caused by optical thin films on the amplitude and phase. Then, the scalar wavefront is extracted from the Jones pupil using the singular value decomposition method, and is used to the wavefront detector and aberration analysis of a Hartmann wavefront detector. The wavefront fitting is performed using Zernike polynomials. Finally, we analyze the reduction of the correction ability of the adaptive optical system.