Global Navigation Satellite System (GNSS) can provide an approach for spacecraft autonomous navigation in earth–moon space to make up for the insufficiency of earth-based tracking, telemetry, and control systems. However, its weak power and poor observation geometry near the moon causes new problems. After the GNSS signal characteristics and satellite visibility were evaluated in Phasing Orbit and Lunar Transfer Orbit, we proposed an adaptive Kalman filter based on the Carrier-to-Noise ratio (C/N0) and innovation vector to weaken the influence of GNSS accuracy attenuation as much as possible. The experimental results show that the spacecraft position and velocity accuracy are better than 10 m and 0.1 m/s near the Earth, and better than 50 m and approximately 0.2 m/s near the moon use GNSS with the proposed adaptive algorithms. Additionally, because of the deterioration of navigation performance based on the orbit filter during orbital maneuvering, we used accelerometer data to compensate for the dynamic model to maintain navigation performance. The results of the experiment provide a reference for subsequent studies.