Abstract: In the context of global climate change, the frequency and intensity of Hourly Heavy Precipitation (HHP) events have been on the rise worldwide, and the hydrometeorological disasters they induce are posing serious threats to sustainable socio-economic development. However, there is still a lack of research examining how the spatial differentiation of heavy precipitation at the hourly scale influences flood processes in small and medium-sized watersheds. To address this gap, the present study focuses on the Ganhe River Watershed (GRW), a representative small mountainous basin located in the middle and lower reaches of the Yangtze River. Long-term (2000–2023) hourly precipitation datasets from four rain gauges and hourly runoff records for 2000–2019 were utilized. A percentile threshold method, applied on a station-by-station basis, was used to define HHP events. Statistical techniques, including trend analysis and seasonal/diurnal cycle analysis, were then employed to examine the multiscale spatiotemporal characteristics of HHP. Furthermore, the influence of HHP spatial distribution on flood processes was assessed by comparing different scenarios of rainfall center location and rainfall pattern. The results indicate that the 98.5th percentile serves as a suitable threshold for defining HHP in the GRW, with station-specific thresholds ranging from 14.50 to 20.00 mm/h, highlighting the pronounced spatial heterogeneity of extreme precipitation regimes across this relatively small basin. In terms of long-term trends, the majority of HHP indices exhibit an upward tendency, and the increasing trends at Wanjia and Daqiao stations are statistically significant at the 0.05 level, suggesting that HHP is intensifying at local scales. In terms of monthly distribution, HHP primarily occurred in June and July. The occurrences of HHP within the day also varied spatially. The peak value of HHP at Wanjia station primarily occurred at 10:00, which is earlier than at other stations, while the peak values of frequency, amount, and contribution at Daqiao station mainly occurred at 13:00, which is earlier than at other stations. Correspondingly, extreme rainfall–runoff events in the basin are also concentrated in June and July, and since 2013 there has been a marked increase in such events, indicating a continuous escalation in extreme flood risk. Compared with all precipitation events, under HHP conditions, the amplification of flood peak discharge and the prolongation of lag time are most prominent when the rainfall center is situated downstream, with increases of 91% and 58%, respectively, highlighting the critical role of storm center location. In the GRW, when an HHP event is recorded exclusively at a single rain gauge station, the spatial position of the storm center within the basin exerts a significant influence on the resulting flood peak magnitude; the location, whether in the headwater area or downstream, can produce markedly different flood magnitudes. Moreover, compared with such single-station events, floods caused by simultaneous multi-station HHP undergo a substantial amplification in both peak discharge and total flood volume, increasing by several times, which reveals a highly nonlinear basin response and underscores the critical role of storm spatial coverage in generating extreme floods. Among various rainfall patterns, the spatially uniform hourly heavy precipitation pattern produces the highest flood peak and represents the primary precipitation type responsible for extreme floods in the GRW. In summary, this study elucidates the spatial differentiation characteristics of HHP in the GRW and their substantial impacts on flood processes. The findings provide valuable insights for deepening the understanding of HHP–flood response mechanisms in mountainous watersheds and offer a theoretical reference for enhancing real-time monitoring, early warning, and flood disaster reduction strategies in the basin. These results highlight the necessity of considering the spatial heterogeneity of HHP in operational flood forecasting and risk mitigation. The study thus contributes to both theoretical knowledge and practical strategies for coping with increasing extreme precipitation in mountainous basins.