[Objective] The relationship between surface freezing/thawing index and runoff over the upper reaches of Heihe River in Western China was discussed in order to provide scientific basis for the runoff prediction and the rational development and utilization of water resources in this basin.[Methods] The impacts of precipitation, air temperature and surface freezing/thawing index on runoff during the period from 1979 to 2006 were investigated over the upper reaches of Heihe River basin in Western China. Changes in freezing/thawing index and river runoff in freezing/thawing period and the relationships between surface freezing/thawing index and runoff were further explored.[Results] There was a significant decrease trend in freezing while a significant increase trend in thawing index, and the most significant change occurred in 1990-2005. The variation of runoff was not obvious in thawing period, while it decreased dramatically in freezing period, especially in winter. The reduction of winter runoff was influenced by the variation in soil seasonal freezing and thawing. The freezing index was reduced significantly, indicating that air temperature increased in seasonal soil freezing process, and more snow sublimated in winter, so that the supply of runoff was reduced. The thawing index increased significantly, leading to a 13~14 cm increase in the depth of seasonal thawing soil, which resulted in an increase of the soil storage space to store part of the groundwater and a decrease in winter runoff.[Conclusion] Changes in the soil seasonal freezing and thawing play significant roles in the runoff of the upper reaches of Heihe River in Western China.