The Hekou-Longmen reach, together with local floods, is the main source area for coarse sedimentations into the Yellow River. When total rainfall slightly increased in the area, discharge dramatically decreased by 40%–70% after the year of 2000, and attracting extensive attention in the context of global climate change. High temporal resolution precipitation (timescales between 1 and 4 h) data from the June to September period from 270 rain gauges over the past three decades was mined in order to help explain the phenomenon. Each rainfall event was classified as light/moderate rain, large rain, heavy rain or rainstorm by the event’s rainfall amount, and further classified as low intensity rain, medium intensity rain and high intensity rain by the event’s rainfall intensity. The Mann-Kendall trend test was applied to detect the presence and significance of monotonic trends, and to find the change points in the mean and variance of the precipitation characteristics series, including the amount, intensity, frequency and duration of each rainfall category. Results show that although the total amount of precipitation has slightly increased, the average rainfall intensity has significantly decreased. The larger change happened in light/moderate rain events and low/medium intensity rain events, and the intensity changes have a great extent occurred around the threshold of Non-Runoff Rainfall regime, which was proposed for the approximate calculation of initial losses. Changes in rainfall distribution between different classes of the Runoff Rainfall regime in the 2000s could lead to 0.9 mm less runoff depth (17.3% of the total reduction) than the 1980–1999 period. The study indicates that changes in hourly precipitation may be responsible for the sharp reduction of discharge.