Based on the polarization transmission theory in optical system, the polarization analysis of a real high numerical aperture (NA) refractive optical lithography system is made, where the anti-reflection coating within current technology, the absorption in coating and base, and polarized illumination are taken into account to obtain a higher-reliability result. Several polarization parameters at every optical interface are calculated, such as transmission, reflection, absorptance and diattenuation, to achieve the effects of anti-reflection coating, absorption of the materials and polarized illumination on transmission performance and imaging performance. The results reveal that the anti-reflection coating can dramatically enhance the performance and stability of this sample system, while reducing the effects of varied polarized illumination to a negligible degree. Besides, the dramatic absorption in the base material plays a main role in the intensity loss, and the absorption has a small contribution to overall polarization effects.