Aerial-aquatic unmanned vehicles are a combination of unmanned aerial vehicles and unmanned submersibles, capable of conducting patrols in both the air and underwater domains. This article introduces a novel aerial-aquatic unmanned vehicle that integrates fixed-wing configuration and flapping-wing configuration. In order to improve the low efficiency of the classic diagonal motion trajectory, this paper proposed an improved diagonal motion trajectory based on joint optimization of the stroke angle and angle of attack curve. The proposed method has been verified through simulations and experiments. A prototype was developed and experiments were completed, both indoors and outdoors, wherein the system’s transmedium transition capability and flapping propulsion performance were comprehensively validated. Additionally, utilizing flapping propulsion, an average underwater propulsion speed of 0.92 m/s was achieved.