The deep space exploration is characterized by long-range exploration targets, long flight time, and big environmental changes, etc. The traditional large loop navigation operating mode based on the ground telemetry, tracking, and station-spacecraft communication commanding can no longer meet the mission requirements in terms of real-time, safety, and reliability. Autonomous navigation technology is an effective means to solve these problems and has become an important direction for the future development of deep space exploration. To ensure mission safety and reliability, a redundant and fault-tolerant design of the key sensitive individual machines is generally required, i.e., autonomous navigation with multi-source fusion. This paper analyzes five aspects of key technologies towards spacecraft multi-source fusion autonomous navigation, including relative dynamics modeling, observability theory, multi-source fusion filtering, error compensation and ground-based experiment validation technologies, and points out the future development trend and focal point of spacecraft autonomous navigation technology based on the demands of autonomous navigation projects implementation and technology development.