As the new members of the Chinese Fengyun-3 meteorological satellites series, the Fengyun-3C (FY-3C) and Fengyun-3D (FY-3D) satellites were launched in 2013 and 2017, respectively. For the first time, both FY-3C and FY-3D satellites carry a high-precision BDS and GPS dual-system space-borne receiver to fulfill their stringent requirement of precise orbit determination (POD). The fusion of BDS and GPS onboard observations can significantly improve the spatial geometry, robustness and reliability of low earth orbit (LEO) POD. In order to achieve high-quality orbit recovery from the onboard GNSS observations, the in-flight calibration of phase center variation (PCV) is a prerequisite. In this contribution, we calibrate the BDS PCV for improving the orbit precision of both FY-3C and FY-3D satellites for the first time. The results show that with the GPS PCV corrections, the residuals of GPS carrier phase observations present a reduction of about 17.6% and 21.9% for FY-3C and FY-3D satellites, respectively, and overlap differences of the GPS-only orbit are reduced on average by 3 and 5 mm. After correcting for BDS PCV, the GPS and BDS combined (GC) POD achieves a better orbit precision for both FY-3C and FY-3D satellites. The application of BDS PCV corrections can contribute to a reduction of up to 12% in BDS phase residuals and a decrease of up to 3 mm in orbit overlap differences in 1-dimension. It indicates that the introduction of the BDS PCV model can significantly improve the orbit precision. Similar orbit precision can be achieved when using the GPS PCV model to replace the BDS PCV model in the GC POD. It demonstrates that for onboard receivers, the GPS PCV model can be used to correct PCV errors of BDS signals, which is commonly used in precise point positioning of ground stations when the BDS PCV is not available. Furthermore, we find that it is feasible to generate an integrated PCV model from both onboard BDS and GPS observations. After application of the integrated PCV model, the FY-3C and FY-3D orbits of GC POD present a better precision than the solution using the single-system PCV model and the largest precision improvement of about 1 mm can be recognized in the radial component. With such a high-quality orbit, FY-3C and FY-3D satellites can be expected to make more contributions to meteorological studies and applications.