Position difference, Doppler observation and time-differenced carrier phase (TDCP) are three commonly used velocity estimation methods. Since the average velocity of two epochs is obtained both in the position difference and TDCP velocity estimation, the accuracy is affected by the carrier's kinematics, large deviation will appear in high dynamic velocity estimation field. While the carrier's real velocity can be obtained in real time utilize the Doppler velocity estimation method, consequently, this method is widely adopted in navigation fields such as vehicle, shipboard and airborne. The accuracy of Doppler velocity estimation will be affected by positioning error through the direction cosine matrix between the receiver and satellite, therefore, high precision position information is the premise to obtain the accurate carrier velocity. The principle of heterogeneous constellations based BDS PPP Doppler velocity estimation is proposed in this paper, and the influence of various errors on the velocity estimation accuracy is analyzed. Based on the high precision position estimated by BDS PPP, the Doppler velocity estimation method is analyzed. The static experimental results show that the velocity estimation accuracy based on BDS PPP position difference is mm/s level, while the Doppler velocity estimation accuracy is cm/s level. In the vehicle dynamic experiment, the velocity estimation results are compared with high precision GNSS/INS integrated navigation results. The results show that the coincidence between the BDS PPP Doppler velocity estimation results and the integrated navigation is cm/s level, while the BDS PPP position difference based velocity estimation is significantly affected by carrier's kinematics, and the coincidence with the integrated navigation results is dm/s level. The Doppler velocity estimation method is recommended in high dynamic applications, the position difference velocity estimation is recommended in low dynamic or low acceleration situations.