Extreme hourly precipitation is amongst the most prominent driving factors of flash floods and geological disasters. Based on the hourly precipitation data of 35 stations in the Three Gorges Reservoir Region (TGRR) from 1998 to 2020, we analyzed the spatiotemporal variation characteristics of hourly extreme precipitation indexes. The selected indicators included the frequency, intensity, period, annual maximum, trend of hourly heavy precipitation (20–50 mm/h) and hourly extreme heavy precipitation (≥50 mm/h) in the TGRR. Closely related climatic factors such as the Western Pacific Subtropical High Intensity (WPSHI) were also discussed. The results showed that in 2010–2020, the cumulative frequency of heavy precipitation magnitude between 25 and 40 mm/h slightly increased, while the corresponding frequency for magnitudes ≥50 mm/h decreased. In summer, the frequency of both heavy and extreme heavy precipitation increased in June and decreased in August, indicating a shift of extreme events to an earlier time in the flood season. The cumulative frequency of heavy precipitation in July had a period of about 7a, and that of extreme heavy precipitation had a period of 3a. The annual average intensity of heavy precipitation and extreme heavy precipitation in the TGRR was 28.9 mm/h and 61.4 mm/h per station, respectively, and both fluctuated and insignificantly decreased from 1998 to 2020. The annual maximum hourly precipitation center in the TGRR moved downstream from west to northeast. The frequency of heavy precipitation was relatively small along the main stream of the river valley. Both the frequency and total amount of heavy precipitation in southeast of the TGRR were significantly higher than those in other regions. Heavy precipitation in the majority of stations with high elevation (higher than 500 m) showed a decreasing trend. The cumulative frequency of precipitation with an intensity of 20–50 mm/h was closely correlated with the Western Hemisphere Warm Pool (WHWP) Index in February and the WPSHI Index in January, and especially, the abnormal large annual frequency (top 20%) showed strong correlation with the two indexes, implying highly predictable factors for extreme events. The frequency of precipitation intensity above 50 mm/h was correlated with the Western Pacific Warm Pool (WPWP) Area Index in January and the WPWP Intensity Index in November of last year. The research results provide a strong and refined factual basis for the assessment and prediction of extreme precipitation, and for disaster prevention and mitigation, in the TGRR.