Abstract: With the diversity and complexity of space exploration missions,the multi-mission and multi-target exploration with single spacecraft of multiple modules is the development trend of space technology. Under normal conditions,the separation signals trigger the continuous autonomous control,which influences the safety of spacecraft and follow-up missions. In this paper,a typical separation signal configuration and a common logical control method based on the trigger of separation signal are proposed aiming at guaranteeing the reliability of separation signal and safety of separation. A mathematical model is set up for on-orbit separation of spacecraft modules as well. Both the model and control method have been simulated,analyzed and tested with practical flight missions. The feasibility and validity of this method are demonstrated for the follow-up flight missions.