Based on the uniform distributed rainfall data in the Hanjiang River basin, the characteristics of spatio-temporal variability of extreme precipitation and flood-waterlogging process are diagnosed in terms of index definition and mathematical statistics. The study found that: (1) no significant trends of extreme rainfall for the entire basin were tested, but there was a jump variation in 1990s from abundance to dryness, accompanied by 20-year main periodic oscillation. Since 2000, the frequency of extremely heavy rain has increased significantly. (2) there is a spatial distribution pattern of lower in the northeast and higher in the southwest, and decreasing from upstream to downstream in the annual means of extreme precipitation. High-value centers are concentrated in the southwestern mountainous areas and the plains in the downstream, which are prone to form the distribution pattern of Central-North Radiation Type and Southeast-Northwest Type. (3) basin usually suffers 5–6 waterlogging processes per year, most of which were light or moderate grade, lasting 2–4 days. Since 2000, the flood-waterlogging process has shown evolution characteristics in increasing of the intensity, frequency, duration, and fluctuation, having strong continuity in the future. (4) affecting by climate and topography, spatial distribution of flood-waterlogging is uneven. Downstream and southwest of upstream are regularly the high-value centers, which are easy to form three kinds of distribution patterns, namely Northeast Radiation Type, Middle-lower Radiation Type and Middle-upper Radiation Type. Since the 21st century, the Hanzhong area and the watershed below Xiangyang both often encountered flood-waterlogging processes of high-intensity, long-duration, and high-frequency, which easy to induce flood disasters. Spatio-temporal variability of extreme precipitation and flood-waterlogging is a direct result of the rational development and utilization of water resources. We expect the results here to provide a deep insight into flood-waterlogging and serve as a reference for the watershed flood disaster response, rain-flood utilization, and optimal allocation of water resources.