In order to solve the problem of lacking of time and space references of the autonomous navigation satellite constellation relying on inter-satellite links, the BeiDou satellite navigation system has introduced ground anchor stations which jointly constitute an integrated satellite-station network with the space satellites. With the constraints of inter-satellite link system, visibility and load quantity, the integrated assignment model of satellite-station/inter-satellite links was established. The shortest information transfer link assignment algorithm based on network layers, and the multi-objective optimization algorithm of ranging link PDOP and network connectivity based on the simulated annealing algorithm were proposed. According to the simulation results, the reference information from the anchor station can be distributed to satellites with the fewest link hops. The PDOP of satellite ranging links is less than 1.4 and close to the lower limitation. The connectivity of the integrated network is better than 3. It is demonstrated that the integrated assignment algorithm can satisfy the requirements of fast information distribution from the anchor station to satellites, ranging for space reference maintenance and network robustness.