Compared with glass-made optical products, polymer injection optical products have the advantages of light weight, easy processing, good impact resistance, and are widely used in high-end fields such as aerospace and precision lenses. However, due to the coupling effect of complex thermal fields and pressure fields in the forming process, injection molded transparent products usually have optical defects such as uneven refractive index distribution, angular deviation, optical distortion and so on. Therefore, the simulation and experimental investigation on the effect of injection molding process on the refractive behavior is of great guiding significance for the manufacture of transparent products with controllable refractive index. In this paper, the layered computational model for the refractive behavior in thickness direction of injection molded optical products was built based on the Hele Shaw injection molding theory and Lorentz Lorenz equation characterizing density and refractive index. The corresponding simulation program with VC++ was developed, and then was merged into the software system Z-Mold, a self-developed injection mould simulation software. Furthermore, the coupling analysis of injection molding filling, packing, cooling and refractive index distribution was successfully implemented based on Z-Mold. Taking the polycarbonate transparent square plate as an example, its refractive index distribution in thickness and flow direction was predicted and analyzed. According to Brewster's law, the refractive index values of square plate at different position were measured. The simulation results were in good agreement with the measured data, which proved that the prediction model for refractive index had high accuracy. This method had been successfully applied to the analysis of the "Shenzhou" extravehicular spacesuits mask.