System Engineering is the scientific method of the plan, research, design, manufacture, test and use, which organize and manage the complex development objects. It is a scientific method of universal significance for all systems. With the increasing complexity for civil aircraft and its system, the development cycle and cost of the system are increasing. The difficulty of quality management, reliability and integration of the system are also getting higher and higher. Model-Based System Engineering (MBSE) uses the method of modeling and graphical expression to deal with the requirements analysis, function analysis, logical architecture design and verification of civil aircraft and system development. This paper firstly describes the idea of MBSE, then analyses its advantages compared with the traditional document-based development process. Finally, a detailed analysis of MBSE used in the requirement analysis of civil aircraft’s brake system is exhibited.