Based on the data of the average rainfall from 1956 to 2013 and the runoff series of the 3 rivers in Qinzhou City over the past 50 years, the sliding average method, linear regression, M-K method and R/S method were used to analyze the tendency and mutation characteristics of the rainfall and runoff. The results show that there is a slow increase trend of the rainfall in Qinzhou City with the increase rate of 0.742mm/10a, and there is a decrease trend of the runoff in the river basins of Maolingjiang, Qinjiang and Dafengjiang with the decrease rates of 0.2 ×108 m3 /10a, 1.1 ×108 m3 /10a and 0.4 ×108 m3 /10a respectively. Molet wavelet analysis was made to get 5 time scales in the rainfall series, of which 22-year and 15-year scales are respectively the first main period and second main period of the rainfall series. There are 3 time scales in the runoff series, of which the 22- year and 8-year scales are respectively the first main period and second main period of the runoff series.