The diurnal variation of precipitation reflects the influence of atmospheric heat and dynamic processes on the water cycle. Using multiple data sets, we carried out case studies and statistical analysis of the diurnal variation in Meiyu rainfall in atypical Meiyu years. Our results show that the morning precipitation was induced by strong southwesterly moisture transport and was mainly composed of stratiform pixels, whereas the precipitation occurring in the afternoon was mainly composed of convective pixels affected by updrafts. The diurnal variation in precipitation in the atypical Meiyu years appeared as a bimodal structure with peaks in early morning (06:30 LST) and afternoon (16:00 LST), which was different from the single morning peak (09:30 LST) in the normal Meiyu years and reported previously. Further research indicated that the morning peak is related to the low-level water vapor flux, whereas the afternoon peak is related to the local solar heating. In addition, the water vapor flux in the Yangtze Plain was characterized by strong morning and weak afternoon fluxes during both normal and atypical Meiyu periods. The diurnal variation in the low-level water vapor flux is thought to be influenced by the intensity of, and distance from, the subtropical high.