The load distribution prediction and design model of the ship’s special mechanical devices and equipment under a nonlinear sea state is a complex and critical issue that directly impacts the ship’s safety, stability, and operational efficiency. This paper first describes the load distribution characteristics of special mechanical devices and equipment in a nonlinear sea state, modeling the nonlinear sea state using the second-order Stokes wave and bimodal Ochi-Hubble wave spectrum. The pump jet propeller is selected as the research object, and the load distribution simulation is carried out by using the CFD-FEM two-way fluid-structure coupling method so as to achieve the prediction and design of the load distribution of the pump jet propeller. Under the wave condition with wave height H=6m and wavelength to length ratio λ/Lpp=0.87, when the ship sailing with 20kn speed facing the waves and the waves are thumping, the measurement points P1~P4 are selected on the pump jet propeller at equal distance, and the loads at the measurement point P4 are more than 3.1kPa.