A civil aircraft safety critical system design scheme using model based systems engineering (MBSE) is proposed in this paper, with considering the civil aircraft/systems design standard and thchnology frontier fields. Considering the availability and integrity of the system functions, civil aircrafts/systems design and safety assessment process are esteblished by using MBSE. Civil aircraft brake system development and assessment scheme are proposed by MBSE tools IBM DOORS and Rational Rhapsody. Use cases, functions flow, and state-machines of the system are set up by corresponding models in requirement analysis, function analysis and design synthesis phases. The system architecture which can guarantee the function availability and safety is designed by fault tree analysis. System models are verified by SysML and Simulink collaborative simulation, and Panel diagram interactive interface.