[Objective] Variations in the interannual and intra-annual runoff of the Pearl River basin from 1960 to 2017 were analyzed in order to provide reference for rational use of watershed resources.[Methods] We used the interannual variation coefficient (C_v) of the runoff, the M-K trend analysis and the Morlet wavelet to analyze the interannual variations in runoff. Meanwhile, we used concentration (period) and runoff contour method for runoff within a year.[Results] The interannual variability of runoff in the Pearl River basin was small and the runoff stability was high. The total runoff had not changed significantly. The change in runoff was coinciding with droughts and floods in the Xijiang and Dongjiang river basins were relatively uniform and the incidence was low, the Beijiang river basin was prone to flood disasters. The runoff in Xijiang, Beijiang, Dongjiang, rivers of the Pearl River basin was basically 25~32, 10~20, 4~10 years. The distribution of runoff in the Pearl River basin was extremely uneven during the year, and in the annual runoff concentration (RCD_year), the Xijiang river was slightly higher than Beijiang and Dongjiang rivers. In recent years, the RCD_year had decreased. The annual runoff concentration period (RCP_year) indicated that the maximum runoff of the Beijiang river alternated in May and June, and the maximum runoff of the Dongjiang river alternated in June and July, and the maximum runoff of the Xijiang river occurred mainly in July.[Conclusion] There is no obvious decline or upward trend of runoff in the downstream areas of the Pearl River basin from 1960-2017, but the interannual and intra-annual changes in runoff are still obvious. The main reason for the change is the vigorous human activities such as the construction of river basin reservoirs.