A storm surge is a complex phenomenon in which current, tide, and waves interact with each other. Even if the wind is the main force of driving the surge, waves and tide are also key factors that affect the momentum and mass transport during the storm surge. Although, the Iranian Makran coastal region in the Gulf of Oman is vulnerable to storms and coastal hazards, the interaction of waves on the storm surge has not yet been studied in this region. This paper aims to investigate tropical cyclone-induced waves and storm surges in the Gulf of Oman through the wave-tide-circulation coupled system. The simulations were carried out using the two-way coupling of wave and hydrodynamic models (MIKE 21 SW + MIKE 3 HD) to compute the wave characteristics and water levels during the super cyclone Gonu, which were validated with the field measurements. Model results, and in particular the water level and significant wave height, agreed well with the observations during the Gonu storm's period. Also, the influences of the key factors interaction (wind, atmospheric pressure, and wave) on a storm surge in the Iranian Makran coasts were evaluated. First, there is a peak surge caused by winds, after that the surges induced by the wave and atmospheric pressure. The wind, pressure, and wave have a contribution of 77.9%, 22.3%, and 10.3%, respectively, in inducing the peak surge of the storm. Key findings of this study indicate the importance of wave-induced setup due to radiation stress as well as the role of the coupled model inaccurate storm surge simulation.