Transmedium vehicles are characterised by high flexibility and strong attack capability, which makes them a key area of current research. However, the transition between air and water remains a critical outstanding issue. The ramjet integrated air–water engine designed in this study is effective and stable in both air and water modes and shows a high degree of adaptability. Using three-dimensional numerical simulations, this study investigates the impact of intake configurations and environmental pressure variations on engine performance, with a focus on the distribution of internal flow field parameters and performance changes during the transition process. The results show that, although the secondary air intake configuration in air mode effectively improves the engine thrust, it causes the front part of the engine to overheat, resulting in a reduction in overall power. The primary intake configuration is more favorable for ensuring a safe transition. During the descent of a vehicle from high altitude, the pressure of the engine’s exhaust tailpipe gradually increases, and the combustion products move to the front of the engine, resulting in a significant loss of power. The entire air–water transition process takes 0.3 s. To ensure the stable transition of the engine’s thrust, this paper proposes a preloaded oxidizer supply control scheme, which injects the preloaded oxidizer within 0.012 s after transition, opens the water intake at 0.205 s, and achieves the engine’s design performance for underwater mode at 0.3 s, after which the oxidizer injection is stopped. This scheme significantly improves the efficiency of the transition process and enhances engine stability. The results of this study provide theoretical support for the design and optimization of air–water transition in transmedium ramjet engines.