The system error of the observation data is the main factor that affects the accuracy of satellite orbit determination. The delay of the satellite transponder is difficult to obtain directly from the orbit measurement, so it has become one of the main sources of the system error of the FY-4A stationary meteorological satellite observation data. In response to this problem, this article first introduces and analyzes the original FY-4A geostationary meteorological satellite transponder time delay calibration scheme, which was found that the solution was unable to obtain satellite transponder delay due to too many parameters to be estimated. Subsequently, a new on-orbit calibration method was proposed that the difference between the time delay of the FY-4A meteorological satellite transponder and the ground correction value was about 2m by using the dynamic precision orbit determination analysis. The results show that the method can effectively retrieve the on-orbit variation of the FY-4A weather satellite transponder.