The Stokes polarimeter based on liquid crystal variable retarders (LCVRs) is a space polarization measurement technology widely used. However, due to the tilt of the optic axis of the LCVR with the driving voltage in the direction of light propagation and the interference in LCVR, the LCVRs-based Stokes polarimeter produces a large instrument polarization, which affects the accurate polarization measurement. In this paper, we combine polarization ray tracing with multi-beam interference, and establish a general three-dimensional polarization analysis model of the LCVRs-based Stokes polarimeter. The simulation results of adjusting the LCVR voltage to reduce the instrument polarization are analyzed, and the variation of polarization measurement accuracy with the field of view before and after optimization of the LCVRs-based Stokes polarimeter is simulated and analyzed. A LCVR structure with additional films for matching the refractive index is proposed. According to the simulation results, this structure can significantly reduce the interference effects and reduce the impact of variations in liquid crystal layer thickness on the interference effects.