The spatial-temporal variability of precipitation is closely related to the occurrence of drought/flood, which thus merits close study. Here we examine the temporal inequality and persistence of precipitation over China from 1961 to 2013, through the use of Gini coefficient, Lorenz asymmetry coefficient and parameters (P00 and P11) of first-order Markov chain. The Mann-Kendall test was also applied to assess the changes in all indices used. The results showed that the temporal inequality of daily precipitation increased, associated with decreased wet days and increased heavy precipitation events, during the past century in most parts of China. The dry spell overall increased while wet spell declined during the period 1961–2013, which implied that the risks of both drought and flood would enhance over China in the future. However, the changes in temporal inequality and persistence of precipitation varied among sub-regions and basins, for example, extreme precipitation decreased in Songhua River basin and Pearl River basin but increased in other basins. The results obtained in this study would be helpful for understanding the spatial-temporal changes of precipitation (and thus drought and flood disasters) and for developing reasonable strategies for water resources management over China under the changing climate.