Nonlinear control strategy is designed to address the problem of modeling uncertainty and complex external environmental interference in crossing water and air media for amphibious buoys. This controller consists of an adaptive backstepping controller and a disturbance observer. Firstly, the medium crossing mechanism of the coaxial water air cross domain flying buoy studied in this article is analyzed and modeled, fully considering some additional variables such as water resistance, buoyancy and its corresponding torque, as well as wave loads. A continuous dynamic model is established by designing a smooth transition function. The backstepping controller forms the foundation of the controller, and the disturbance observer enhances the robustness of the closed-loop system by estimating the lumped uncertainty that is difficult to measure. Meanwhile, an adaptive algorithm is introduced to compensate for the remaining residuals of the disturbance observer. The combination of adaptive algorithms and disturbance observers improves the robustness of the system. The stability of closed-loop systems is proven using Lyapunov functions. Finally, Simulink simulation is conducted on the proposed controller, and the results show that even in the presence of disturbances and uncertainties, the designed controller has strong suppression ability against unknown disturbances, effectively demonstrating the superiority and robustness of the proposed method.