This article focuses on the problem of high-intensity vibrations in autonomous underwater vehicles (AUVs) in high-speed and high-pressure conditions. A dynamic modeling method for simplified AUVs with variable cross-section shaft is studied and experimentally verified. Firstly, the FEM of propeller-shaft-shell system by Lagrange method is established, which concludes the main components like propellers, motors, shafts, bearing supports, cylindrical shells and others. The shaft and cylindrical shell are both modelled using Timoshenko beam elements, the nonlinear factors of bearing based on Hertz contact theory are also added. The resonance frequency and system dynamic response are calculated, and their amplitude frequency characteristics and inherent characteristics are both analyzed. Secondly, the Runge-Kutta method is used. By comparing two designs (a uniform rotation shaft vs. a variable cross-section rotation shaft), the dynamic characteristics are analyzed by post-processing signals such as time domain response, spectrum, trajectory diagram and amplitude-frequency response. It is found that the maximum amplitude in the middle shell unit of the model of the variable cross-section rotation shaft decreased by about 30%. Finally, experiments are designed to verify the feasibility of the FEM model, which are matched the simulations reasonably well, with results staying within 20% error. In addition, comparing with the frequency spectra under different excitation frequencies, it can be clearly observed that there is a frequency doubling phenomenon in the model, indicating that the vibration characteristics of the system are affected by the excitation frequency. The theoretical model in this article reveals the dynamic response characteristics of AUVs, it can provide new improvement ideas for the optimization design of vibration and noise reduction of AUVs.