Space on-orbit service vehicles have important applications in tasks such as on-orbit maintenance, life extension and orbital debris removal of spacecraft, GNC subsystem plays an important role in the task completion process. Due to the large differences in the dynamic characteristics of the target aircraft and the requirements of the task, there are many uncertainties in the process of task completion, it needs to take into account the needs of energy security, attitude safety, anti-collision safety, etc. GNC needs to plan different task conditions according to different target characteristics. This paper defines the GNC mission architecture model of the on-orbit service vehicle, and uses software-defined technology to implement task autonomous management under various working conditions. Colleagues realize the safety of the whole vehicle in fault mode through early warning mechanism.