The water air amphibious tilting multi rotor unmanned ships was subject to complex and variable surface fluid forces during cross domain operations in a multi fish pond environment, resulting in significant fluctuations in the ship’s attitude and flight altitude. In order to improve the attitude stability of unmanned ships during surface takeoff, a model compensation based linear self disturbance rejection surface takeoff control method was proposed. Firstly, a detailed dynamic modeling of the multimodal unmanned ship was conducted. Secondly, considering the attitude changes during the takeoff process on the water surface, a real-time attitude estimation model and buoyancy estimation model was proposed based on unmanned ships. Then, a linear self disturbance rejection attitude and altitude controller based on model compensation was designed. Finally, a linear active disturbance rejection controller based on model compensation was designed. In the simulation experiment, compared with the PID algorithm, the proposed method reduced the roll convergence time by 66.7% and the roll fluctuation by 98.3%, reduced convergence time on the x-axis by 34%, reduced convergence time on altitude by 41.2% and the fluctuation on altitude by 80.0%. The simulation results verified the effectiveness and stability of the proposed method. In practical experiments, the unmanned ship achieved takeoff from the water surface with a flying altitude of 1.2m, fluctuations of roll less than three degrees, and a fluctuation of pitch and yaw less than two degrees. The experimental results showed that the proposed control algorithm effectively improved the stability and antiinterference ability of the water air amphibious tilting multi rotor unmanned ships during the water air cross domain process.