The Lightning Mapping Imager (LMI) onboard the Fengyun-4A (FY-4A) satellite is the first independently developed satellite-borne lightning imager in China. It enables continuous lightning detection in China and surrounding areas, regardless of weather conditions. The FY-4A LMI uses a Charge-Coupled Device (CCD) array for lightning detection, and the accuracy of lightning positioning is influenced by cloud top height (CTH). In this study, we proposed an ellipsoid CTH parallax correction (ECPC) model for lightning positioning applicable to FY-4A LMI. The model utilizes CTH data from the Advanced Geosynchronous Radiation Imager (AGRI) on FY-4A to correct the lightning positioning data. According to the model, when the CTH is 12 km, the maximum deviation in lightning positioning caused by CTH in Beijing is approximately 0.1177° in the east–west direction and 0.0530° in the north–south direction, corresponding to a horizontal deviation of 13.1558 km, which exceeds the size of a single ground detection unit of the geostationary satellite lightning imager. Therefore, it is necessary to be corrected. A comparison with data from the Beijing Broadband Lightning Network (BLNET) and radar data shows that the corrected LMI data exhibit spatial distribution that is closer to the simultaneous BLNET lightning positioning data. The coordinate differences between the two datasets are significantly reduced, indicating higher consistency with radar data. The correction algorithm decreases the LMI lightning location deviation caused by CTH, thereby improving the accuracy and reliability of satellite lightning positioning data. The proposed ECPC model can be used for the real-time correction of lightning data when CTH is obtained at the same time, and it can be also used for the post-correction of space-based lightning detection with other cloud top height data.