Evolution of hydrological cycle and water resources has been a hot topic for scholars and researchers around the world. This holds even more true in water source areas under changing environments. In this paper, the evolution characteristics of runoff in source regions of Yangtze River were investigated using statistical methods. On this basis, the impacts of both surface meteorological factors and upper atmospheric circulation factors on runoff were evaluated. Results show that runoff at Zhimenda station in the headwaters of Yangtze River distributed unevenly during a year, and a significant increasing trend is observed with regard to annual runoff. An obvious abrupt change in the year of 2004 was observed for runoff time series from 1956 to 2016. Wavelet analysis indicated that there were two significant periods of these time series, which were 7-8 years and 20-21 years, respectively. The biggest power of the spectrum was observed in the 42-43 year period. As for the impacts of different meteorological and atmospheric factors on runoff, our study indicated that precipitation was the leading driving force for runoff variation, and the role of water surface evaporation was also important.The variation of runoff was also influence by air temperature, but the effect was not significant enough. There was good agreement between monthly runoff observations of Zhimenda station and the Tibetan Plateau Index_B (TPI_B). Both the spatial distribution and magnitude of precipitation agreed well with the Tibetan Plateau vortex.