Inundations in low-lying coastal areas are commonly caused by compound flooding due to the combination of surge overflow and wave overtopping. The increasing frequency of strong tropical cyclones accompanied by high waves is exacerbating flooding risks. In recent studies, wave-induced flooding (i.e., wave run-up and overtopping) has been reported as a critical component of coastal inundations. However, no clear standard has been established for estimating compound flooding caused by the nonlinear interactions of each component. The present study developed a fully coupled model of surge, wave, tide, and wave overtopping to propose a framework for assessing compound coastal inundations. A series of numerical experiments were conducted in an idealized coastal area to analyze flooding risk comprehensively. The experimental results revealed that the conventional decoupled calculation processes for wave overtopping/run-up tend to overestimate the inundation. The advanced approaches provided stable estimations of offshore wave characteristics that change dynamically under extreme wave conditions, resulting in a reliable wave overtopping calculation. Furthermore, a considerable amount of inundation can occur even when typhoons make landfall during low tidal conditions due to the prolonged occurrence of wave overtopping. The proposed framework can be considered an optimal method for practical flooding risk assessments in coastal areas by estimating compound inundations and including transition processes of surge overflow and wave overtopping/run-up.