The temperature inversion inconsistency phenomenon is analyzed for the on-orbit IR calibration of Visible and InfraRed Radiometer (VIRR) which is a payload onboard polar-orbiting meteorological satellite FY-3C. A specific methodology, i.e., the whole chain automatic simulation and analysis, is proposed. This method involves the orbital parameters and the satellite platform environment. By means of the ray trace of the opto-mechanical structure with high precision, the quantified effect of solar stray light is obtained. The simulation includes on-orbit IR calibration and solar incidence, resulting in the identification of the incidence path of solar stray light as well as the explanation for the temperature inversion inconsistency. Through the comparison between the simulated results and the on-orbit data of the satellite, the effectiveness and the validity of the method are verified. This method can be applied to the simulation and analysis of on-orbit stray light effect of the same-typed payloads. This work can also provide references to the recalibration of historical data.