The BeiDou satellite navigation system (BDS) is different from other global navigation satellite systems (GNSSs) because of its special constellation, which consists of satellites in geostationary earth orbit, inclined geosynchronous earth orbit (IGSO), and medium earth orbit (MEO). We have estimated the phase center offsets for BeiDou-2 IGSO and MEO satellites with a direct PCO parameters model, and constraints are applied to cope with the correlation between the PCOs and other parameters. Validation shows that the estimated PCO parameters could be used to improve the accuracy of orbit and clock offset overlaps. Compared with the Multi-GNSS Experiment antenna phase center correction model, the average improvements of the proposed method for along-track, cross-track, and radial components are 19 mm (31%), 5 mm (14%), and 2 mm (15%) for MEO satellites, and 13 mm (17%), 12 mm (21%), and 5 mm (19%) for IGSO satellites. For clock offset overlaps, average improvements of standard deviation and root mean square (RMS) are 0.03 ns (20%) and 0.03 ns (12%), respectively. The RMS of precise coordinates of the BeiDou-2 positioning was also improved significantly with a level of 24 mm (30%) in the up-direction. Compared to MEO satellites, the observations of IGSO satellites cover only a small range of nadir angles. Therefore, the estimation of phase center offsets (PCOs) of IGSO suffers from high correlation with other estimation parameters, and the accuracy of IGSO PCOs is lower than that of MEO. Meanwhile, the initial PCOs of the new-generation named BeiDou-3 were estimated by using a limited number of stations of about 10, and the performance of new PCOs was discussed.