With the networking completion of the Beidou navigation satellite system (BDS-3), the BDS-3 system was opened in the whole world on July 31, 2020. It is important practical significance to analyze the performance of the BDS-3 system and the GPS in terms of satellite common view timing comparison. In order to analyze the accuracy of timing comparison for BDS-3/GPS global navigation satellite system common view time, the comparison experimental of BDS-3/GPS with medium and long baseline is carried out based on satellite common view algorithm by using the National Metrology benchmark system of atomic time scale maintained by National Institute of Metrology (NIM), China. The timing model and algorithm of the BDS-3/GPS satellite common view algorithm are deduced in detail, and the stability of receiver clock difference and accuracy analysis of timing comparison for the BDS-3/GPS based on the satellite common view algorithm are compared and analyzed. The experimental results show that the stability of receiver clock difference of BDS-3 and GPS is respectively ns-level, but the stability of receiver clock difference of BDS-3 system is slightly better than that of GPS; the accuracy analysis of timing comparison for BDS-3 and GPS based on satellite common view algorithm is respectively better than 24 ns, but the accuracy analysis of timing comparison for BDS-3 system is slightly better than that of the GPS.