The positioning of highly elliptical orbit (HEO) spacecraft is very important in deep space exploration and other missions. The Beidou Navigation Satellite System (BDS-3), which was completed in 2020, has put forward new ideas for using GNSS technology to make up for the lack of earth-based TT&C systems. At the same time, the selection of the gravity field order and the perturbation forces must be considered when using dynamical methods for HEO spacecraft positioning. In this paper, simulation experiments are carried out based on the Two-Line Orbital Element (TLE) data of BDS. Two HEO satellites with different semimajor-axis (67509.6 km, 212857.3 km) are selected as the target spacecraft orbits. The single point positioning (SPP) method and Extended Kalman Filter (EKF) method are used for HEO spacecrafts positioning respectively. The experiments show that a 20×20 order gravity field model can be chosen for the orbital integral of HEO spacecraft orbits, and the integration error caused by solar gravity and lunar gravity should be taken into account with the change of orbital altitude. Adding Geostationary Orbit (GEO) and Inclined GeoSynchronous Orbit (IGSO) navigation satellites improved the visibility of these two orbits by 19.45% and 16.64%, respectively, and improved the GDOP value by 14.1% and 3.8%, respectively, compared to observing MEO satellites only. The use of the EKF method can effectively improve the positioning accuracy of the HEO spacecraft compared to the SPP method. For the spacecraft in HEO-1, the RMS value of the positioning errors of the EKF method was 67.82 m, and the accuracy of each direction was improved by 44.28%, 38.85%, and 38.62%, respectively. For the spacecraft in HEO-2, the positioning errors in the x direction of EKF method was within 12 km and within 2 km in the y and z directions. The accuracy of these three directions was improved by 84.91%, 79.24%, and 58.64%, respectively.