Using the monthly hydrological and meteorological observational data in the source regions of the Yangtze River and the NCEP/NCAR reanalysis monthly data from 1960 to 2011, the variation characteristics of the runoff in the source regions of the Yangtze River and its climate cause have been analyzed by a variety of analytical methods in this paper. Results show that the annual mean runoff and runoffs in summer, autumn and winter had a persistent declining trend in the source regions of the Yangtze River before 2005, and the annual mean runoff and seasonal mean runoffs have a notable increasing trend in the source regions of the Yangtze River after 2005; especially in summer, the increasing trend is very obvious. In a long-term, the annual mean runoff in the source regions of the Yangtze River varies obviously, with quasi-periods of 4-year and 12-year. The plateau summer monsoon, the surface sensible heat in the source regions from July to August, precipitation, evaporation, temperature and the meltwater from snow and glaciers have evident contribution to the variation of runoff. After 2005, the annual and seasonal precipitations in the regions have increased notably, but the annual and seasonal evaporations in the regions have decreased significantly; the meltwater from snow and glaciers has increased due to temperature increasing notably; all of these have caused runoff sharp increase in the source regions of the Yangtze River since 2005. Under the above background of climate change, the runoff has sharply increased in the source regions of the Yangtze River since 2005.