The coordinate reference misalignment caused by ship angular deformation is an important factor affecting the operational performance of shipborne weapons and equipment. Based on the local inertial measurement units (IMUs) distributed on the ship and the deformation law of ship mechanics, the whole ship deformation prediction can be realized. The influence of local reference number and installation location on the accuracy of deformation prediction is studied in this paper. The simulation results show that when the installation position of the ship local IMU can better reflect the ship vibration model characteristics, four sets of local inertial reference can be used to predict the angular deformation at any point of the whole ship by the least square estimation method. The interpolation prediction error is less than 2.5″ (1σ), and the extension prediction error is less than 5″ (1σ).