Climate warming leads to frequent extreme precipitation events, which is a prominent manifestation of the variation of the global water cycle. In this study, data from 1842 meteorological stations in the Huang–Huai–Hai–Yangtze River Basin and 7 climate models of CMIP6 were used to obtain the historical and future precipitation data using the Anusplin interpolation, BMA method, and a non-stationary deviation correction technique. The temporal and spatial variations of extreme precipitation in the four basins were analysed from 1960 to 2100. The correlation between extreme precipitation indices and their relationship with geographical factors was also analysed. The result of the study indicates that: (1) in the historical period, CDD and R99pTOT showed an upward trend, with growth rates of 14.14% and 4.78%, respectively. PRCPTOT showed a downward trend, with a decreasing rate of 9.72%. Other indices showed minimal change. (2) Based on SSP1-2.6, the intensity, frequency, and duration of extreme precipitation changed by approximately 5% at SSP3-7.0 and 10% at SSP5-8.5. The sensitivity to climate change was found to be highest in spring and autumn. The drought risk decreased, while the flood risk increased in spring. The drought risk increased in autumn and winter, and the flood risk increased in the alpine climate area of the plateau in summer. (3) Extreme precipitation index is significantly correlated with PRCPTOT in the future period. Different atmospheric circulation factors significantly affected different extreme precipitation indices of FMB. (4) CDD, CWD, R95pD, R99pD, and PRCPTOT are affected by latitude. On the other hand, RX1day and RX5day are affected by longitude. The extreme precipitation index is significantly correlated with geographical factors, and areas above 3000 m above sea level are more sensitive to climate change.