Understanding the spatiotemporal variability of extreme hydrologic events, especially those driven by typhoons over Asia, and their controlling factors is essential to testing and predicting their future changes under global warming. Here, we present a series of direct heavy-rainfall records over the past ca. 10,000 years based on lake sediments from a volcanic cone (Sara Oreum) on Jeju Island, Korea, where orographic amplification of precipitation is dominant and sensitive to present typhoon activity. The reconstructed heavy rainfall index based on the high-resolution elemental ratios (e.g., Ti/Al and Sr/Si) shows clear variability at centennial timescales and is similar to records of coastal flooding events along the southern coast of Korea, typhoon-driven overwash events along the south-western coast of Japan, indicating strong typhoon influence on the heavy rainfall events in Jeju Island during the Holocene. Furthermore, this heavy rainfall-typhoon linkage has been influenced by past El Niño–Southern Oscillation (ENSO) activity and sea surface temperature (SST) in the western Tropical Pacific, showing time-varying influences. This study suggests that on decadal to multi-centennial timescales, stronger ENSO activity is responsible for eastward shift in the location of typhoon genesis, resulting in more frequent recurving tracks of typhoon and increased landfalls in Korea and Japan, whereas SST affects the intensification rate of typhoon. The heavy rainfall index reconstructed from the volcanic cones of Jeju Island may be used as an indicator of past frequency and track changes of typhoon over highly populated East Asia.