In order to build the flight system functional architecture of aircraft mission requirements, the model-based systems engineering (MBSE) method is used and improved during the section of concept design, and the forward engineering process is cleared for key crucial architecture for civil aircraft system. The typical mission scenario of the civil aircraft “emergency go-around” is used as a case. By identifying the functional requirements of the typical civil aircraft, the method constructs the functional requirement architecture based on the human-machine joint simulation experiments, records the confirmation process of the demand, realizes the capture requirements, unpacks the functional black box, verifies the completeness and rationality of requirements by the state machine based on MBSE, ultimately ensures the traceability of the functional design process capturing the functional requirements. The method is applied to one type of complex system represented by aircraft, while it effectively transforms the customer’s fuzzy requirements into concrete realized functions, perfects system functional architecture and satisfies the technical requirements of higher levels.