To solve the problem of lack of early reliability evaluation in complex system design process, a MBSE (model-based system engineering) method was proposed to support the design and reliability evaluation of complex systems. With the characteristics of complex system development, a MBSE modeling method based on MOFLP-R(mission, operation, function, logic, physics and reliability) was proposed to support design and reliability assessment of complex system. KARMA, a system modeling language based on GOPPRR(graph, object, property, point, relationship and role), 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.