Although typhoons frequently impact the northwestern Taiwan Strait, how coastal valley topography regulates upwelling dynamics during typhoons remains unclear. This study employs a numerical model to investigate how a coastal valley influences upwelling processes during Typhoon Soudelor. The results show that the storm surge temporarily disrupts the upwelling-induced low sea surface height and generates coastal trapped waves (CTWs). The storm surge also produces a strong offshore pressure gradient, which is partially damped by the valley. Driven by typhoon-induced alongshore currents, valley-induced cold water shifts southwestward. Meanwhile, intense turbulent mixing weakens stratification, and the valley constrains the onshore penetration of typhoon-induced downwelling circulation. After the typhoon, sea level and circulation in the upwelling region recover to pre-typhoon conditions within approximately 2 days, whereas restratification requires 4–5 days, with a longer recovery time inside the valley. Furthermore, the valley amplifies low-frequency cross-shore currents generated by CTWs and suppresses the energy of near-inertial and diurnal tides in the alongshore currents. This study highlights the influence of irregular coastal topography on storm surge and upwelling dynamics under typhoon conditions.