Abstract: The Middle Route of the South-to-North Water Diversion Project is a major inter-basin water transfer project in China designed to alleviate water shortages in northern regions. It has been in operation since December 2014, with its water source area located in the Danjiangkou Reservoir and its upstream areas. Extreme precipitation events carry considerable implications for its water resource security. This study analyzed the characteristics of extreme precipitation events during the rainy season (May–October) in the water source area using daily precipitation data from 1961 to 2021. Subsequently, future projections for the near term (2026–2050) and long term (2071–2100) were conducted using daily precipitation estimates from 12 models under 3 Shared Socioeconomic Pathways (SSP1-2.6, SSP2-4.5, and SSP5-8.5) of the Intergovernmental Panel on Climate Change’s Coupled Model Intercomparison Project Phase 6 (CMIP6). Considering model precipitation biases, the quantile delta mapping bias correction algorithm was applied before projections. The results reveal the following: (1) In the past 61 years, precipitation frequency (RD) decreased while heavy rain days (Rr25) and extreme precipitation (R95PTOT) increased. Precipitation intensity (SDII) increased substantially at the rate of 0.19mm d⁻¹ (10 a) ⁻¹, especially in Ankang and its upstream regions between the Daba Mountains and the Qinling Mountains. According to the moisture budget diagnosis, the vertical moisture advection term made the dominant contribution to the increase in SDII, with the largest contribution from the dynamic term, followed by the nonlinear term. (2) Rr25, maximum 1-day precipitation (Rx1day), R95PTOT, very extreme precipitation (R99PTOT), and SDII experienced an interdecadal shift in the late 1970s, followed by a significant increase during the 1980s. (3) Compared with the reference period (1961–2014), under low (medium and high) emission scenarios, Rr25 increased by 10.8% and 19.0% (5.0% and 19.2%; 7.9% and 31.8%) for the near and long term, respectively, and R95PTOT increased by 8.8% and 8.7% (1.1% and 12.7%; 8.6% and 25.1%), respectively. Spatially, the most pronounced increases in extreme precipitation occurred in the Funiu Mountains and the Danjiangkou Reservoir. In summary, analyses of observational data over the past 61 years and future projections from CMIP6 indicate that total precipitation during the flood season in the water source area shows an increasing trend, which is beneficial for the sustainability of the South-to-North Water Diversion Project. However, the increase in extreme precipitation poses challenges for water resource management and engineering safety.