The ranging systematic error is the main factor that affects the orbit determination accuracy of geostationary earth orbit (GEO) satellites. The geostationary characteristics of GEO satellites make the ranging data systematic error. Especially for the station systematic error, it has a strong correlation with the satellite orbit. Therefore, the independent means must be used to solve. The simulation data are firstly used to analyze the impact characteristics of ground systematic error and on-board systematic error on the orbit. The FY-4B satellite ranging system is taken as an example to analyze the measured range data. The analysis results show that there is an abnormal systematic error in the FY-4B ranging system. To determine the source of this system error, a series of schemes are designed. Through experiments, the systematic error is not from the ground or the satellite. And it is determined that the systematic error of the FY-4B comes from the satellite. The orbit determination estimation is utilized to calculate the on-board systematic error to calibrate it. The calibrated observation data are used to achieve orbit determination, and the residual error of each station is reduced from 15 m to 2 m. The orbit determination accuracy is improved from 800 m to 20 m. The analysis results show that the method of calibrating the systematic error on the satellite through the orbit determination estimation is practical and effective.