In the two most recent decades, more frequent drought struck southern China during autumn, causing an unprecedented water crisis. We found that the increasing autumn drought is largely attributed to an ENSO regime shift. Compared to traditional eastern Pacific (EP) El Niño, central Pacific (CP) El Niño events have occurred more frequently, with maximum sea surface temperature anomalies located near the dateline. Southern China usually experiences precipitation surplus during the autumn of EP El Niño years, while the CP El Niño tends to produce precipitation deficits. Since the CP El Niño has occurred more frequently while EP El Niño has become less common after the early 1990s, there has been a significant increase in the frequency of autumn drought. This has implications for increasing precipitation shortages over southern China in a warming world, in which CP El Niño events have been suggested to become more common.