Based on the monthly runoff data and meteorological data of the Weigan River Basin during 1960 -2013, the intra - annual and inter-annual runoff change characteristics of the Weiganhe River Basin in recent 54 years were analyzed by using Kruskal-Wallis test, R/S analysis, ensemble empirical mode decomposition (EEMD). The results show that (1) In the basin in recent 54 years, there were larger Cv and Cr of runoff, uneven distribution of inter-annual runoff, the runoff in summer > that in autumn > that in spring > that in winter, and this trend would be more obvious in the future; (2) There were 3 significant stages of intraannual runoff change characteristics, i.e. wet season from 1960 to 1976, normal season from 1976 to 1993 and drought season from 1994 to 2013; (3) The runoff presented a growth trend in the whole period, especially in summer, however experienced a slight drop in winter, and the runoff would keep going up in near future; (4) The temperature and precipitation increased in the last 54 years, the fluctuation points appeared in the late 1970s and early 1990s, which are consistent with variation characteristics of runoff. The runoff is effected by precipitation in summer and by temperature in autumn and winter.