The shape optimization considering both aerodynamic and radar stealth performances has been a considerable attention area for next-generation aircraft, with challenges involving balancing design contradictions and improving optimization efficiency. This paper develops a surrogate-based integrated design optimization method coupling Computational Fluid Dynamics (CFD) and Computational Electromagnetics (CEM) for aerodynamic/stealth performance enhancements. The topology-based 3D hexahedral mesh generation and 2D triangular mesh generation with adaptive refinement provide efficient preprocessing for CFD/CEM solvers. The surrogate-based optimization algorithm with parallel infill-sampling strategy and adaptive design space expansion is employed to search the global optimum and improve optimization efficiency while filtering out numerical noise. The Weighted Sum method is employed to address design contradictions in different disciplines. Optimizations considering aerodynamic, stealth, and aerodynamic/stealth performance of a flying wing aircraft are conducted to verify the effectiveness of the developed method. The optimization results indicate that exclusive consideration of a singular discipline leads to a significant deterioration in the performance of the other discipline. Balanced performance is achieved through coupling optimization. The numerical noise in the stealth discipline is markedly higher than in the aerodynamics discipline. The results demonstrate that the developed method is capable of addressing aerodynamic/stealth design optimization problems and significantly reducing the number of CFD/CEM evaluations while maintaining global optimization effectiveness.