According to hydrological surveying data of 57 years of from 1956 to 2012, this paper used the methods such as dist anc average analysis, concentration rate, concentration period, coefficient of uniformity to analyze runoff variation feature and trend of the source regions of the three river since the ecological protection project wasimplemented in 2005. The results showed that space runoff distribution of the source regions of the three river increased from south to north from 2005 to 2012; distance average of runoff decreased from southeast to northwest from 2005 to 2012, the maximum was in source area of the Yangtze River, distance average was more than 80%, the minimum was in source area in southeastern regions, distance average was in about 10%; the runoff concentration rate, coefficient of uniformity presented decreasing trend, and the concentration period was delayed. The source area runoff was in overall wet station from 2005 to 2012. The runoff of each station has significantly increase more than annual average. The runoff has clear upward trend in Yangtze River, and has no significant upward or downward trend in the Lancang River and the Yellow River source region during 1956 to 2012.