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This paper establishes the flight control system model using the Harmony-SE method, and realizes simulation of the aeronautical weapon trajectory from the launching point to the target point. The characteristic of flight control system of aeronautical weapon is that all functions revolved around the calculation and iteration of system state. Since the main idea of Harmony-SE is to design the system architecture and system function based on use cases, there are redundant steps such as analyzing the context of use cases in the process of modeling the system with this characteristic, which is inefficient. To solve this problem, this paper puts forward an optimization method. On the basis of Harmony-SE, this paper optimizes the architecture analysis and design method based on the function flow in the Harmony-SE method, simplifies the system model architecture, proposes the architecture design method based on the information flow, which simplifies Harmony-SE steps by using the information flow to suture function flow, thus improve the modeling efficiency of the flight control system.