To research the stern flap (SF) and waterjet–hull interaction, unsteady Reynolds-averaged Navier–Stokes (URANS) simulations for a waterjet-propelled trimaran considering sinkage and trim are performed. Uncertainty analysis of the numerical results for the bare hull (BH) model is presented. At the design speed Froude number (Fr) of 0.6 and under displacement state, the model-scaled trimaran, installed with stern flaps of varied angle and length, tests the BH and self-propulsion (SP) performance based on URANS simulations. For the resistance, the global effects due to motions and the local effects of SF, waterjets (WJ), and the coupled term between SF and WJ on the hull are separately analyzed. Taking the waterjet propulsion system into account, an SP model with reasonable stern flap effectively reduces the trim, the resistance acting on the hull and the waterjet thrust deduction which contributes to energy-saving and high-efficiency propulsion. The mechanism of the improved performance of the waterjet-propelled trimaran with stern flaps is discussed. For the resistance increment, the global effects, the local effects of SF and WJ are the major reason for resistance increase, and the nonlinear coupled term of local effects contributes to the resistance reduction most. In addition, the different resistance components of frictional, hydrostatic, and hydrodynamic are separately researched, which shows that the pressure resistance components plays a leading role in the total resistance reduction in the SP model with the suitable SF.