Active vibration control (AVC) can solve many vibration problems. However, structural vibration in underwater vehicles often involves other factors such as complex excitation and path coupling, etc. At present, the traditional algorithm (e.g., multi Filtered-x Least Mean Square, M-FxLMS) usually cannot effectively process the multi-frequency excitation and the coupling effects of the multi-secondary path, which will affect its convergence and stability to a certain extent. Consequently, a novel strategy is presented in this paper, namely, the wavelet packet transformation decentralized decoupling M-FxLMS algorithm (WPTDDM-FxLMS), which can solve the structural vibration problems mentioned above. The multi-frequency control is converted into a single-frequency line spectrum control, and the feedback compensation factor is introduced in the identification of the secondary path, both of which can simplify the multi-path control system to the parallel single-path systems. Furthermore, the WPTDDM-FxLMS algorithm is applied to the AVC in a multi-input and multi-output system (MIMO) vibration platform. Finally, the simulation and experiments show that the wavelet packet can decompose the multi-frequency excitation into a line spectrum signal, and the improvement of the decentralized decoupling and the variable step-size can effectively reduce the computation amount and increase the convergence speed and accuracy. Overall, the novel algorithm is significant for multi-path coupling vibration control. It will have certain engineering application value in underwater vehicles.