As an underwater thruster, the pump-jet propulsor (PJP) exhibits low radiation noise but generates significant line spectral noise in the low-frequency band. In this paper, we equipped the PJP hub with two types of propeller boss cap fins (PBCF): one fixed and the other rotating with the rotor. The hybrid large eddy simulation and Reynolds-averaged Navier–Stokes method, along with the Ffowcs Williams-Hawkings (FW-H) equation, are employed to systematically analyze the hydrodynamics, exciting force, flow noise, and flow field of PJPs. The results indicate that the fixed PBCF improves the hydrodynamic performance and reduces the exiting force, raising the rotor's thrust coefficient by 9.22%–14.99%. The fixed PBCF also modifies the characteristics of line spectrum noise but causes an increase in the flow noise. The rotating PBCF increases the rotor's thrust coefficient by 2.03%–3.15%, decreasing both exciting force and line spectrum noise. For instance, at the advance coefficient of 0.8, its sound pressure level at the rotor frequency drops to 49.6%. Additionally, the rotating PBCF increases the pressure of the hub wake and effectively reduces the hub vortices' strengths. This paper provides a theoretical foundation for designing PJPs that enhance concealment and minimize vibrations and noise.