Runoff change is closely related to climate and human activities, and the interaction between them changes the water cycle of the basin. So the quantitative analysis of climate change and human activities can serve as a reference for the regulation of water resources efficiency and the coordination of agricultural development in the basin. Taking the upper reaches of Wujiang River as the research object, based on the long-term series of measured runoff and meteorological data from 1960 to 2013 of Yachi River Hydrological Station and a total of 12 weather stations in the basin and its periphery, the abrupt changes of precipitation and runoff were recognized using Mann-Kendall and cumulative anomaly method, and the characteristics of the periodic change of runoff was analyzed using Morlet wavelet method with the emphasis on the effects of human activities and precipitation on runoff change in the upper reaches of Wujiang River. The results indicated that from 1960 to 2013, there was no significant increase in runoff and precipitation, two abrupt changes of both occurred in 1986 and 2002 with synchronized characteristics and phases during this period. The resonant periods of runoff and precipitation were 18-19 a and 19-20 a respectively. The runoff of the basin had a certain lagging effect on precipitation changes, and the lag time was 1 to 2 a. Taking 1960-1986 as the base period, the contribution of precipitation and human activities on runoff from 1987 to 2002 was 50.93% and 49.70%, whereas it was 49.30% and 50.70% from 2003 to 2013, respectively. The impact of precipitation on runoff was decreasing whereas that of human activities was increasing. Therefore, the water resources management should focus on the construction and regulation of benign human activities in the future.