Tropical cyclones affecting Shenzhen city have shown a remarkable tendency to increase in both intensity and quantity, highlighting the urgency of accurate forecasts of storm surges and flooding for effective planning and mitigation. Utilizing satellite and field observations together with the advanced high-resolution baroclinic wave–current model (SCHISM), a comprehensive investigation aimed at storm surge and flooding in Shenzhen was conducted. Statistical work of historical tropical cyclones revealed that Shenzhen was most vulnerable to cyclones propagating from the southeast toward the northwest and passing Shenzhen down the Pearl River Estuary. Thus, a representative, i.e., super typhoon Hato (2017), was selected for further study. Validations of numerical results suggested satisfactory model performance in mapping the wave, tide, and surge processes. Remarkable differences in spatiotemporal distribution and intensity of storm surge and flooding were found along the Shenzhen coast, which was dominated by the propagation of far-field surge and tidal waves, cooperation between wind direction and coastline orientation, estuary morphology, and the land terrain. Intervention of wave–current interaction improved the simulation of the surge and flooding and triggered an earlier occurrence time of the maximum surge in specific areas. The Pearl River discharge significantly elevated the sea level height inside the estuary and contributed to a more severe surge. Given the extremely complicated river networks and huge freshwater flux of Pearl River and the increasing trend of concurrent heavy precipitation of tropical cyclones, future investigations on compound flooding were suggested.