Abstract: Flying wing is a widely applied configuration for advanced military aircraft. Not only should aerodynamic and stealth requirements be taken into account at its conceptual design stage, but also the flight control system should be well designed. A flying wing aircraft was investigated, and the strategy and methods for integrated control-aerodynamic-stealth were studied. A new flow suitable for conducting multi-objective optimization in each discipline-s subspace was proposed. Design variables in subspace were assigned based on disciplinary analyses, and then system level design variables were formed by variable synthesis. According to the characteristics of flying wing configuration, control allocation based control system architecture was adopted, and time domain indexes were used as objectives and constraints in control discipline. Results of optimization show the effectiveness of new methods, which supply a feasible way for incorporating control discipline into the multidisciplinary design optimization of flying wing configuration aircraft.