To solve the problem of lack of early reliability evaluation in complex system design process, a model-based system engineering (MBSE) method is proposed to support the design and reliability evaluation of complex systems. With the characteristics of complex system development, a MBSE modeling method based on "Mission, Operation, Function, Logic, Physic and Reliability" (MOFLP-R) was proposed to support design and reliability assessment of complex system. KARMA, a system modeling language based on "Graph, Object, Property, Point, Relationship and Role" (GOPPRR), was used to express the MOFLP-R process. Then, in order to evaluate the reliability of the complex system, the code generation was used to map the diagram to the numerical model. Finally, the method was applied to a hydraulic system case and the results showed that the proposed method is effective for complex system design and evaluation.