Intersatellite Link (ISL) technology helps to realize the auto update of broadcast ephemeris and clock error parameters for Global Navigation Satellite System (GNSS). ISL constitutes an important approach with which to both improve the observation geometry and extend the tracking coverage of China’s Beidou Navigation Satellite System (BDS). However, ISL-only orbit determination might lead to the constellation drift, rotation, and even lead to the divergence in orbit determination. Fortunately, predicted orbits with good precision can be used as a priori information with which to constrain the estimated satellite orbit parameters. Therefore, the precision of satellite autonomous orbit determination can be improved by consideration of a priori orbit information, and vice versa. However, the errors of rotation and translation in a priori orbit will remain in the ultimate result. This paper proposes a constrained precise orbit determination (POD) method for a sub-constellation of the new Beidou satellite constellation with only a few ISLs. The observation model of dual one-way measurements eliminating satellite clock errors is presented, and the orbit determination precision is analyzed with different data processing backgrounds. The conclusions are as follows. (1) With ISLs, the estimated parameters are strongly correlated, especially the positions and velocities of satellites. (2) The performance of determined BDS orbits will be improved by the constraints with more precise priori orbits. The POD precision is better than 45m with a priori orbit constrain of 100m precision (e.g., predicted orbits by telemetry tracking and control system), and is better than 6m with precise priori orbit constraints of 10m precision (e.g., predicted orbits by international GNSS monitoring & Assessment System (iGMAS)). (3) The POD precision is improved by additional ISLs. Constrained by a priori iGMAS orbits, the POD precision with two, three, and four ISLs is better than 6, 3, and 2m, respectively. (4) The in-plane link and out-of-plane link have different contributions to observation configuration and system observability. The POD with weak observation configuration (e.g., one in-plane link and one out-of-plane link) should be tightly constrained with a priori orbits.