Wind forcing makes a vital contribution to the hydrodynamic loads on structures at sea. The flow physics is complex, involving interactions among surface water waves, turbulent wind, and semi-submersed object. We perform a simulation-based study on a canonical problem of wind past a semi-submersed rectangular prism with the focus on the wave effect, which is an essential factor in wind loads at sea but has been elusive. To tackle this problem, we develop a hybrid simulation method consisting of two parts: a precursor simulation of coupled wind and wave motions in the far field upstream to provide physical inflow condition, and a near-field simulation of the air and water motions around the object. The simulation method is validated through numerical tests and comparisons with data from the literature for different aspects of the code. This hybrid simulation method is then applied to study the effect of surface wave motions on the wind load on the object. Various wave conditions are considered, including pure wind-sea satisfying the Joint North Sea Wave Project spectrum as well as wind-sea mixed with long-wavelength ocean swells. The simulation results exhibit significant oscillations in the wind load on the object. The oscillations are found to correlate well with the incident wave motions and are particularly strong in the presence of swells. The underlying mechanism is explained through analyses on variations of wind speed with different wave phases and wave-correlated flow patterns of the wind when it impinges on the object. Our simulations also indicate that waves have an appreciable effect on the wake behind the object.