A multi-bump strategy combines automatic optimization and flow control and is employed in airframe/intake–exhaust integration design of flying wing. The numerical simulation method of -Re{macron}t transition model is verified and used for optimization and validated analysis. According to flow features of basic integration configuration, the multi-bump strategy is proposed. Based on the strategy, the optimization framework is constructed and applied to the design. The research results show that the present method has good design effectiveness. The cruise lift-drag ratio improves 4.1% and longitudinal static stability increases 1.1% at large attack angle. The multi-bump strategy is a skillfully deflected means to improve aerodynamic performance.