The El Niño Southern Oscillation (ENSO) creates strong variations in sea surface temperature in the eastern equatorial Pacific, leading to major climatic and societal impacts1, 2. In particular, ENSO influences the yearly variations of tropical cyclone (TC) activities in both the Pacific and Atlantic basins through atmospheric dynamical factors such as vertical wind shear and stability3, 4, 5, 6. Until recently, however, the direct ocean thermal control of ENSO on TCs has not been taken into consideration because of an apparent mismatch in both timing and location: ENSO peaks in winter and its surface warming occurs mostly along the Equator, a region without TC activity. Here we show that El Niño—the warm phase of an ENSO cycle—effectively discharges heat into the eastern North Pacific basin two to three seasons after its wintertime peak, leading to intensified TCs. This basin is characterized by abundant TC activity and is the second most active TC region in the world5, 6, 7. As a result of the time involved in ocean transport, El Niño’s equatorial subsurface ‘heat reservoir’, built up in boreal winter, appears in the eastern North Pacific several months later during peak TC season (boreal summer and autumn). By means of this delayed ocean transport mechanism, ENSO provides an additional heat supply favourable for the formation of strong hurricanes. This thermal control on intense TC variability has significant implications for seasonal predictions and long-term projections of TC activity over the eastern North Pacific.