Precise information about the phase center corrections (PCCs) for BeiDou satellite antennas is not only essential to the generation of high-precision orbit and clock products but also important to the determination of terrestrial scale. However, the existing BDS PCCs still suffer from some deficiencies, such as the lack of phase center variations (PCVs) for several BDS satellites as well as the misalignment of phase center offsets (PCOs) and the latest IGS20 frame. We present the estimation results of both PCVs and PCOs for all 37 currently in-service BDS Inclined Geosynchronous Satellite Orbit (IGSO) and Medium Earth Orbit (MEO) satellites. The results demonstrate that the nadir-angle-dependent PCVs of the same satellite block type have fairly good consistency. The horizontal PCO estimates and the igs20.atx values have a consistency of several centimeters. As for the Z-PCOs aligned to IGS20 frame, the estimated values are 2380 and 530 mm smaller than the igs20.atx values for BDS-2 IGSO and BDS-2 MEO satellites, while those of BDS-3 MEOs have mean differences of −61 and 46 mm with respect to igs20.atx values for satellites manufactured by the China Academy of Space Technology and Shanghai Engineering Center for Microsatellites, respectively. By using the estimated PCCs instead of the igs20.atx values, the precise orbit and clock determination precision can be improved by 5–32% and 4–20%, respectively. Furthermore, applying the estimated PCCs, the scale factors determined by BDS solutions exhibit good consistency with IGS20 frame, with mean scale differences below 0.15 ppb.