To keep the global navigation satellite system functional during extreme conditions, it is a trend to employ autonomous navigation technology with inter-satellite link. As in the newly built BeiDou system (BDS-3) equipped with Ka-band inter-satellite links, every individual satellite has the ability of communicating and measuring distances among each other. The system also has less dependence on the ground stations and improved navigation performance. Because of the huge amount of measurement data, the centralized data processing algorithm for orbit determination is suggested to be replaced by a distributed one in which each satellite in the constellation is required to finish a partial computation task. In the present paper, the balanced extended Kalman filter algorithm for distributed orbit determination is proposed and compared with the whole-constellation centralized extended Kalman filter, the iterative cascade extended Kalman filter, and the increasing measurement covariance extended Kalman filter. The proposed method demands a lower computation power; however, it yields results with a relatively good accuracy.