Beidou-3 Global System Satellite carries the Ka inter-satellite link load. Facing the reality of the on-board environment, the distributed autonomous orbit determination strategy of all constellations is studied. The distributed autonomous orbit determination algorithm under the constraints of long-term forecast ephemeris is deduced, and the relationship between anchorage station setting strategy and orbit determination accuracy is analyzed. The simulation results of full constellation show that under the constraints of long-term forecast ephemeris, the average URE of 60-day orbits is limited to less than 4 m, but URE is still accumulating. 3 Anchorage stations are the optimal scheme in quantity, which can make the average URE converge to 0.5 m in 0.54 days. In the selection of anchorage station location, high latitude anchorage station has no contribution to improve the accuracy of autonomous orbit determination, and low latitude single anchorage station can control URE at about 1 m.