The stratospheric airship, with long-endurance and quasi-static capability, is suitable to carry out special mission such as communications relay, hot spots monitoring, etc. In order to improve the safety performance of the stratospheric airship and keep the robustness of mission, health management (HM) system is introduced, the foundation of which is the logic architecture. Based on the analysis of three options about the logic architecture used in spacecraft, hierarchical fusion architecture is selected, the functional modules in which are designed in detail. To solve urgent faults, moreover, the autonomous intelligent control system (AICS) is introduced. Meanwhile, monitoring mission is taken as an example to discuss the mission health management strategy based on laser communication.