This study introduces the third-generation BeiDou Navigation Satellite System (BDS-3) system’s creative global operation and service architecture based on regional stations and Ka-band inter-satellite links (ISLs). The architecture’s contributions to BDS-3 include not only combined orbit determination and time synchronization but also autonomous orbit determination and time synchronization, global operations and services. The BDS-3 on-orbit operation results are being presented in the paper to verify the designed capabilities. Compared with BDS-2, the orbit determination accuracy is improving from 0.6 m to 0.15 m, and the time synchronization accuracy is improving from 6.67 ns to 1.16 ns. Under autonomous orbit determination and time synchronization, the 30-day orbit maintenance accuracy reaches 16 m, and the time synchronization accuracy reaches 3.74 ns. The success rate of data transmission reaches 99%, and the delay is better than 12.9 s. In the future, laser ISLs will be used to enhance the system structure and further improve global operation and service capabilities.