The observed runoff data at Tuotuo river and Zhimenda river hydrometric stations in the source region of Yangtze River from 1978 to 2009 are analyzed through Mann-Kendall test and Relevant Analysis method to research the runoff sequence variation. Results show that the maximum annual runoff at both stations has an increasing trend. The maximum runoff increased remarkably in Tuotuo river but unobvious in Zhimenda river. Significant correlation was found between the maximum runoff variation at these two stations, which suggests that the variation of runoff extremum from 1978 to 2009 is mainly affected by warm and wet climate,vegetation coverage variation, and the increase of precipitation.The research result could be of great value for the planning of river source protection, water resource protection, flood prevention and dry season response.