This paper employed a direct URANS CFD based approach to investigate the speed loss and waterjet performance for a waterjet-propelled trimaran in short-crested head waves. Firstly, a reasonable quantity of linear superposed regular waves was validated to simulate the realistic ocean wave adopted on the ITTC directional wave spectrum. Then the wave parameters were applied to the URANS CFD simulations, to avoid the wave reflection due to structures and to narrow the simulation domain, the Euler Overlay Method (EOM) based wave forcing zone was defined in the outer domain, the time history of the wave elevation and the wave patterns matched well with the theoretical results. Moreover, by employing the PID-controller and Body-Force method, the 1/30 scale waterjet-propelled trimaran free-running numerical model was validated through the trimaran model tests. Eventually, the free-running simulations in short-crested head waves of the trimaran were performed considering the effects of sea state, traveling speed, and wind, respectively. The added resistance in short-crested waves was mainly caused by the pitch and heave variation, and lead to the speed loss and waterjet performance deterioration. Notable, the wind-induced speed loss could account for nearly one half of the total while the wind speed exceeds the vessel speed. The proposed approach of direct evaluating the traveling and propulsion performance in short-crested waves shows reasonable results and practical value.