Rainfall, tide, and wave overtopping can together cause inundation in some coastal areas. However, there have been few cases of inundation analysis considering compound flooding due to the difficulty of the interdisciplinary technique. The purpose of this study is to suggest an analysis technique of compound flooding in coastal areas that links flow simulation tools of coasts and watershed. XP-SWMM was used to analyze rainfall–runoff simulation and 2D surface inundation analysis. A coupled model of ADCIRC and SWAN (ADCSWAN) was used for analyzing expected flow, including wave spectrum, tide, and storm surge from the distant ocean, and the FLOW-3D model was used to estimate the flow and wave overtopping in the coastal area. The analysis technique was applied to Marine City located in Busan, the Republic of Korea, where rainfall and wave overtopping occurred simultaneously during typhoons, and the results were reasonable. The study results are meaningful as they can contribute to the improvement of reproducibility of real phenomena of compound flooding in coastal areas through linked application of flow simulation tools of coasts and watershed.