In recent years, many low-orbit satellites have been widely used in the field of scientific research and national defense in China. In order to meet the demand of high-precision satellite orbit in China’s space, surveying and mapping, and other related fields, navigation satellites are of great significance. The UKF (unscented Kalman filter) method is applied to space targets’ spaceborne GPS autonomous orbit determination. In this paper, the UKF algorithm based on UT transformation is mainly introduced. In view of the situation that the system noise variance matrix is unknown or the dynamic model is not accurate, an adaptive UKF filtering algorithm is proposed. Simulation experiments are carried out with CHAMP satellite GPS data, and the results show that the filtering accuracy and stability are improved, which proves the algorithm’s effectiveness. The experimental results show that the Helmert variance component estimation considering the dynamics model can solve the problem of reasonable weight determination of BDS/GPS observations and effectively weaken the influence of coarse error and improve the accuracy of orbit determination. The accuracy of autonomous orbit determination by spaceborne BDS/GPS is 1.19 m and 2.35 mm/s, respectively.