Abstract The emergence of inter-satellite link (ISL) technology, which realizes the high-precision measurement of the inter-satellite distances and forms a spatial geometric constraint within the constellation, enables the high-precision autonomous orbit determination of the GNSS satellites. Firstly, according to the fact that ISL adjustment is singular to the satellite orbit state vector, a distributed autonomous orbit determination algorithm employing the long-term forecast ephemeris to constrain the constellation orientation is designed in this paper. Then, the autonomous orbit determination using 60-day onboard ISL observations of the whole constellation is carried out. Then, the resulting orbits accuracy is evaluated by comparing them with a precise orbit determination using a global reference network with an accuracy of 0.10 m. The results show that the mean root mean square (RMS) of the user range error (URE) over a 60-day period of the 24 BDS-3 satellites in the constellation is 3.22 m. The characteristics of orbit errors for individual satellite are very similar, which is mainly caused by the overall orientation errors of the constellation. After eliminating these orientation errors, the corresponding mean RMS of URE is reduced to 0.68 m. The prediction errors of the Earth rotation parameters and the determination errors of the parameters of the state vectors, which compose the orientation errors, are further investigated. The Earth rotation parameter prediction errors mainly cause errors in the estimates of the longitude of ascending node, of which the 60-day error can reach 2.5e-5°. The determination errors of the parameters of the state vectors -- the inclination and the right ascension of ascending node, can reach 2.4e-5° and 5.1e-5° rad, respectively.