In order to deeply know the effects of climate change on river runoff where precipitation main happened in winter, and guide the reasonable development utilization of the local water resources, the hydrological characteristics and climatic variation law were analyzed, and based on the construction of Three - source Xin'anjiang Watershed Hydrological Model and setting of different climate scenarios, the response of water resources on the rivers of winter rain type to climate change was discussed. The results revealed that precipitation mainly occurred in winter and spring, summer precipitation was less than normal in Vakhsh River Basin, precipitation had little effect on runoff, and temperature directly determined the level of runoff. Precipitation showed a weak upward trend and the temperature showed an increasing trend in mountainous and plain areas, however, warming trend was more obvious in plain areas than the mountains. By constructing hydrological model and setting different climate scenarios, it can be found that the runoff was more sensitive to the temperature change than precipitation; river runoff was significantly increasing along with the temperature increasing. The most obvious changes of monthly average runoff occurred in April, May and October, which had the most significant increase in April and October, and has the most obvious reduce in May.