In high-orbit space missions, the significant attenuation of Global Navigation Satellite System (GNSS) signals due to long transmission distances and complex environmental interferences has led to a drastic degradation in the accuracy of traditional positioning models, which has attracted great attention in recent years. Although multi-system GNSS fusion positioning can alleviate the problem of insufficient satellite visibility, the existing methods are difficult to effectively cope with the challenges of multi-source noise coupling and inter-system error differences unique to high orbit. In this paper, we propose an adaptive GNSS positioning optimization framework for a high-orbit environment, which improves the orbiting reliability under complex signal conditions through dynamic weight allocation and a multi-system cooperative strategy. Different from the traditional weighting model, this method innovatively constructs a two-layer optimization mechanism: (1) Based on BP neural network, it evaluates the noise characteristics of pseudo-range observations in real time and realizes the adaptive suppression of receiver thermal noise, ionospheric delay, etc.; (2) it introduces Helmert variance component estimation to optimize the weighting ratio of GPS, GLONASS, BeiDou, and Galileo and reduces the impact of signal heterogeneity on the positioning solution of the multi-system. Simulation results show that the new method reduces the root-mean-square error of positioning by 32.8% compared with the traditional algorithm to 97.72 m in typical high-orbit scenarios and significantly improves the accuracy loss caused by the defective satellite geometrical configurations under multi-system synergy.