We analyse the change trends of the annual and seasonal runoff series of the hydrological station Batang on the headstream of the Yangtze River over the period 1960–2007. The relations between runoff series and precipitation and temperature conditions are investigated, and the influence of the refreezing process of meltwater of the glaciers on the Yangtze River flow is examined with the proposed accumulated temperature deficit (ATD) index. It is found that annual runoff at the Batang station is not stable during the period 1960–2007. From 1960 to 1980, there was a rather strong decrease of 14.4 m3 s−1 year−1 on average in spite of the statistically significant increase in air temperature and rather stable precipitation. It is argued that the annual rate of glacier runoff generation is possibly controlled by the ATD rather than by the direct air temperature. Seasonal analysis indicates that ATD might be of greater influence in autumn and winter in affecting runoff than in spring and summer. The research in this paper may be helpful in understanding how the hydro-climatic conditions affect runoff generation in the cold regions.