In many countries, thunderstorms are the main contributor to hourly extreme precipitation (HEP). Prior studies have shown that the number of thunderstorms decreased steadily in whole country of China, however, HEP increased significantly in several areas over the past half-century. The role of thunderstorms in changes in HEP occurrence remains largely unknown in China. In this study, for the first time, we used continuous 32-year records of hourly precipitation and thunder, and the fifth-generation European Centre for Medium-Range Weather Forecasts atmospheric reanalysis, to analyze changes in thunderstorms under various vertical wind shear (VWS) environments, and their contribution to HEP occurrence. The number of HEP events associated with thunderstorms (TD-HEP) increased significantly in southern China (SC) but decreased significantly in northeastern China (NEC) and east of the Tibetan Plateau (ETP). Weak VWS thunderstorms accounted for 69.1% of TD-HEP in SC. Changes in the most unstable convective available potential energy and precipitable water (PW) in SC favored an increase in weak-VWS thunderstorms, which resulted in a 2.35 h warm-season−1 increase in overall “station-mean” TD-HEP events from 1980 to 2011. As the major contributor to HEP in NEC, moderate-VWS thunderstorms decreased by 0.37 h warm-season−1 due mainly to a reduction in PW, leading to a negative trend in TD-HEP events. Similarly, the decreasing TD-HEP occurrence on the ETP was due to a decrease of 1.12 h warm-season−1 of moderate-VWS thunderstorms. Studying the VWS environments of thunderstorms, and changes therein under a warming climate, can improve understanding of the changes in HEP in China.