Satellite antenna phase center offset (PCO) correction is essential not noly for L-band ground-tracking GNSS high-precision data processing, but also for Ka-band inter-satellite link (ISL) observations. The Ka-band ISL and L-band satellite-ground observations of 90 days from 25 November 2020 to 23 February 2021 are used for the Ka-band PCO estimation and precise orbit determination (POD) validation for BDS-3 satellites. The results show that the standard deviations of the estimated Ka-band PCOs for 29 BDS-3 satellites are 1.73, 2.63 and 3.58 cm in the X, Y and Z components, respectively. The accuracy of the Ka-band PCO estimates for medium Earth orbit satellites (MEO) is better than those of inclined geosynchronous orbit (IGSO) and geostationary Earth orbit (GEO) satellites due to a better observation geometry. The POD validation results indicate that using the estimated Ka-band PCOs can improve the ISL-based orbit determination performance. Using Ka-band ISL and L-band satellite-ground observations with 40 global stations for combined POD, the orbit overlap comparison shows that the average three-dimensional (3D) root mean square (RMS) error for 29 BDS-3 satellites is decreased from 12.6 to 6.6 cm with a reduction of 47.6%, and satellite laser ranging (SLR) validation for 4 BDS-3 satellites shows an accuracy improvement from 6 to 5 cm in RMS. When using ISL and only 7 regional ground stations are used, the average 3D RMS of orbit overlap errors is decreased from 15.9 to 10.9 cm with a reduction of 31.6%, and the RMS of SLR residuals for 4 BDS-3 satellites is decreased from 6.7 to 5.6 cm. For ISL-only POD, the average 3D RMS of orbit overlap errors is decreased from 18.0 to 12.4 cm with a reduction of 31.1%, and the RMS of SLR residuals for 4 BDS-3 satellites is decreased from 7.1 to 6.9 cm.