Hot droughts, defined as droughts concomitant with high temperatures, pose a greater threat to water resources than droughts alone. However, the hydrologic responses to hot droughts and their changes under climate warming remain unclear. Using multiple observational datasets and projections from the latest Earth System Models (ESMs), we assess the impacts of hot droughts on runoff in the Yangtze River Basin (YRB) from the historical period (1961–2023) to the future period (2031–2100). An unprecedented hot drought during the 2022/2023 hydrologic year, with an estimated return period exceeding one thousand years, offers a unique opportunity to investigate the mechanism of hydrologic responses to hot droughts. Both the heat and the drought were the most severe over 1961–2023, resulting in pronounced hydrologic anomalies, including a 25% decline in runoff. However, the runoff was not the lowest over the same period, partly due to the extra water storage from the preceding wet year. The frequency of hot drought years is expected to increase by 13.6%/10.4% under the SSP2-4.5/SSP5-8.5 scenario during 2031–2100 relative to 1961–2023, despite increasing precipitation. Runoff during hot drought years is projected to decrease by 3.3%/5.2% under the SSP2-4.5/SSP5-8.5 scenario compared to that in the historical period. Although the YRB is known for its abundant water resources, our results show that the densely populated subbasins (including the Jialing River, Han River, Wu River, Dongting Lake, and Poyang Lake Basins) are projected to experience water scarcity during hot drought years when insufficient runoff is available to meet water demand. These results underscore the water security threatened by increasing hot droughts and call for improved strategies of water resources management to mitigate the climate change impacts.