The ocean response to the passage of Typhoon Morakot (2009) near the continental shelf of the East China Sea off northeastern Taiwan was evaluated using a numerical ocean model to clarify how the permanent upwelling feature in this region was changed during this storm event. Several studies have identified the presence of the Kuroshio subsurface water in this Cold Dome region, which results from the interactions among the monsoon, the Kuroshio and the shelf topography. This study shows how tropical cyclone Morakot's passage quickly disturbed the circulation around Taiwan and induced a short-period intrusion of the Kuroshio water onto the continental shelf. The intrusion began during the second half of the forced period and lasted for approximately two days. The upwelling and northward flow were greatly enhanced during this period, allowing the subsurface water from the upstream Kuroshio to be transported onto the shelf and to reach the Cold Dome. The intrusion-induced cold anomaly along the north coast of Taiwan was much more significant than what can be achieved by local vertical mixing. The cold anomaly later formed an eddy, which gradually propagated with the Kuroshio to the northeast.