This study proposes a design method for integrated vehicle/engine systems with variable-geometry inlets based on the Gaussian pseudospectral method. By establishing a multilayer framework integrating propulsion system modeling, flight dynamics modeling, and control law optimization, the inlet control problem is transformed into an objective function optimization problem under specific flight trajectories. Results indicate that control law must ensure maximum thrust across the entire speed range in the minimum time climbing mode, while specific impulse optimization is prioritized in the minimum fuel consumption mode. Further multivariable optimization reveals that the optimal inlet configuration is independent of flight trajectory and determined by the propulsion system characteristics. For the same inlet configuration, different flight trajectories only affect the aircraft’s acceleration parameters. This work provides a theoretical foundation and methodological framework for the integrated design of advanced wide-speed-range aircraft, with significant implications for the development of next-generation high-speed flight vehicles.