Thermal wakes discharged by a body moving under the ocean contain large amounts of thermal energy and form a specific temperature profile upon reaching the sea surface. These surface thermal signatures play a vital role in the infrared remote sensing of marine underwater targets. In this study, a model is developed for simulating thermal wakes out of an underwater moving body. The model is based on the 3-D dynamic meshing technique and volume of fluid method, and the surface thermal signatures and buoyant trajectory are analyzed. In addition, a velocity-inlet wave-generating method is coupled with the simulation model, and the influence of gravity waves on the buoyancy and diffusion processes of thermal wakes is investigated. The results show that the velocity-inlet wave-generating method exhibits good performance in wave generation with the period error δT = 0.18%, and wave height error δH = 5.88% (for the second-order Stokes wave). Gravity waves suppress the buoyancy of thermal wakes, resulting in a % increase in the underwater buoyancy distance. The wave enhances the heat transfer of the thermal wake with surrounding water, which causes the surface maximum temperature difference to decrease by 5.6%, and the temperature distribution of the thermal wake becomes more uniform with a broader area.