A comparative study on the wake dynamics of a pump-jet propulsor (PJP) and a ducted propeller (DP) is conducted to investigate the effects of the pre-swirl stator and corresponding stator–rotor interaction on the wake evolution and destabilization mechanisms of a PJP system. The flow field analysis, vortex structure identification, and dynamic mode decomposition (DMD) analysis are carried out based on the numerical results obtained from delayed detached eddy simulations. The numerical hydrodynamic loading and flow field of the PJP are compared with experimental results, and they are in good agreement. Compared with the DP, the stator trailing vortices of the PJP interact with the rotor trailing vortices as well as the hub vortex, accelerating their diffusion and viscous dissipation. The pre-swirl stator triggers the generation of secondary vortices and moderates the spiral behavior of tip leakage vortices, which dominates the wake instability of PJP. The DMD analysis revealed that the wake field evolution is primarily characterized by the different mode structures at blade passing frequency and its multiples, especially in the PJP due to its strong stator–rotor interaction. The modal energy decays faster in the PJP wake field owing to its more turbulent and earlier instability. The hub vortex plays an important role in the wake dynamics of the DP.