A fluid-structure interaction method based on computational fluid dynamics and finite element analysis was employed for conducting numerical simulation of vehicle-propeller combined models to investigate the structural deformation law of an elastic propeller in the complex wake field of a vehicle and the effect of this deformation on excitation forces. Based on the characteristics of both uniform and non-uniform submarine wake fields obtained through harmonic analysis, the steady and dynamic deformation characteristics of the elastic propeller under different wake fields were analyzed. The rigid and elastic propellers were compared in terms of the time-averaged value and the fluctuating amplitude of excitation forces, so as to analyze the underlying mechanism by which the structural deformation affected the excitation forces. The experimental results showed that steady deformation of the elastic propeller was mainly driven by the time-averaged load in the wake field, and the increased pitch angle led to a 9.5% rise in the time-averaged axial force. The dynamic deformation, which was mainly driven by the fluctuating load in the non-uniform wake field, could buffer the inflow excitation and provide adaptive regulation, thus significantly suppressing the pulsating amplitude of the propeller’s axial excitation force at the blade frequency with a reduction of 86.1%. This study reveals the regulatory mechanism of structural deformation of elastic propellers on excitation forces and provides theoretical support for the application of marine propulsion systems and the control of excitation forces.