Surface waves perform a crucial role in modulating tropical cyclone (TC) systems and have proved to be key for numerical TC predictions. In this study, we investigate the effects of wave-induced mixing and wave-affected surface exchange coefficients using a coupled ocean–atmosphere–wave model for two real TC cases: Shanshan (2018) and Megi (2010). The results demonstrate that wave-affected surface exchange coefficients enhance air–sea heat fluxes and have a significantly positive effect on simulated TC intensity, size, and strengthening process. In contrast, the wave-induced mixing has a negative impact on TC intensity and size and is not conducive to TC intensification and maintenance. The net effect of these two factors is a balance between the wave-affected positive contribution and the negative contribution from wave-induced sea surface temperature cooling. We find that the effect of wave-induced mixing on a TC system depends on the local thermal structure of the ocean. When the thermocline is weak and there is warm water at the wave-induced mixing penetration depth, the negative effect of the wave-induced mixing is weak. However, when there is cold subsurface water and a strong thermocline, wave-induced mixing has a significant impact, which exceeds the wave-driven positive feedback.