Typhoon Maria was a devastating super typhoon hitting China in 2018. We conducted five numerical experiments based on the Coupled Ocean–Atmosphere–Wave–Sediment Transport model system to explore the sensitivity of typhoon track, intensity, structure, and oceanic response to the feedbacks of ocean surface waves (particular attention was paid to wave-induced sea surface roughness [SSR]), and different planetary boundary layer (PBL) parameterization schemes. The model results were in good agreement with observations. It was found that Typhoon Maria's intensity and structure, especially the distribution of air-sea interface heat flux and the shape of the typhoon centre, were highly sensitive to the feedbacks of waves, the choices of PBL and wave-induced SSR parameterization schemes. Previous model results based only on atmospheric models have shown that typhoon simulation accuracy is very sensitive to the parameterization scheme of PBL. In this study, it was revealed that the effect of wave feedbacks on typhoon simulation results could be comparable to that of using different PBL parameterization schemes. The wave feedbacks include the modification of the SSR and the additional cooling induced by wave-enhanced ocean mixing. From the sensitivity experiments, the former was the most dominant, and its main mechanism lies in the correction of the SSR to affect the exchange coefficients of momentum and heat fluxes at the air-sea interface and ultimately the typhoon simulation results. A systematic analysis of sea temperature response during typhoon was conducted, and the response showed small difference in different experiments. This suggests that the difference in typhoon intensity and structure among the experimental simulations is not significantly related to the difference in simulated sea surface temperature, but is most likely related to the difference in momentum and heat fluxes caused by wave feedbacks and the choices of PBL and wave-induced SSR parameterization schemes. The difference of significant wave height (SWH) in experiments with different wave-induced SSR parameterization schemes reached 10% (1.5 m). The typhoon-induced sea surface height (SSH) reached 2.4 m, and the difference of SSH caused by wave feedbacks, different PBL and wave-induced SSR parameterization schemes reached 12.5%, 12.5% and 8.3%, respectively. This study has significant implication for improving the simulation accuracy of typhoon track, intensity, structure, and disasters caused by typhoons.