A submarine's hydrodynamic performance is critical, as it directly influences its stealth, maneuverability, and endurance. A numerical investigation is conducted on a SUBOFF model equipped with a pump-jet propulsor (PJP) under varying inflow velocities. The numerical results demonstrate strong agreement with those reported by Posa et al. and Huang et al. verifying the reliability of the computational model. The energy loss calculated using the integral entropy generation rate method aligns with the results obtained from the total pressure loss method, with a maximum error of 8%, thus confirming the effectiveness of the entropy generation theory. The inflow quality of the propulsor is evaluated through the velocity non-uniformity ξ and perpendicularity Θ. The distribution of non-uniformity shows circumferential variation, particularly near the SUBOFF wall, which influences the hub and blade roots of the PJP. In addition, the entropy generation rate is distributed throughout the flow field surrounding the SUBOFF, within the PJP, and in the wake region. Elevated entropy generation rates are primarily located near the wall and in regions exhibiting specific flow structures. In addition, the energy dissipation characteristics of particular flows are clarified by analyzing typical vortex structures such as the hub passage vortex and tip leakage vortex, along with their relationship to the distribution of entropy generation rate. This provides new insights into flow field diagnostics based on entropy generation theory, contributing to the optimization of submarine design and enhancing its overall combat capability.