To meet the requirement of time-varying inertial parameter identification of control algorithms for shipborne Stewart wave compensation platforms, this study proposes an innovative inertial parameter identification method based on a non-inertial system. Unlike traditional Stewart identification methods with a fixed frame, the proposed method does not require designing excitation trajectories to consider the condition number of the observation matrix. Namely, the proposed method requires only performing two-dimensional dynamic parameter collection for parameter identification in a six-dimensional non-inertial motion. In addition, a coupling error dimension reduction method is developed to improve the identification accuracy under the condition of coupling motion. Finally, experiments are conducted to verify the effectiveness of the proposed identification method. The experimental results show that under the coupling motion conditions, the coupling errors of the corrected singularity points are reduced by 7.9–28.1% compared to before correction, and the axial force average error correction is below 5.32%.