At present, the safe operations of spacecraft are facing severe challenges due to the increasingly congested orbital space and intensified space competition, which poses new challenges to the ability of spacecraft to autonomously cope with orbital threats while carrying out established missions, and at the same time, brings new development opportunities to intelligent autonomous control technologies of spacecraft. Under such a circumstance, after summarizing the current trends of orbital threat perception, spacecraft autonomous decision-making and planning, collision avoidance maneuvers, and autonomous control system architecture design, we analyze the main bottleneck problems in the intelligent autonomous control for spacecraft confronting orbital threats, and then propose that developing the integrated “perception-decision-action” control system is an effective means to solve the bottleneck problems. Furthermore, we systematically discuss the basic theoretical issues that need to be addressed in the intelligent autonomous control of threat avoidance from the aspects of integrated control system modeling, design, analysis and verification.