Based on the surface runoff, temperature and precipitation data of the Hailar River from 1958 to 2008, in this paper, using the method of linear trends of change, the long-term trend of time series of surface runoff was investigated, and then the varying characteristics of annual and decadal runoffs in this region were obtained. Using precipitation and runoff double-mass curve of the Hailar River, the impact of changes in precipitation and permafrost on runoff was also analyzed. It is found that the runoff of the river had a decreasing trend from 1958 to 2008, with high flow during the period from the 1980s to the 1990s and low flow after the 2000s. Runoff in spring and autumn had decreased while in winter had increased obviously, and precipitation in winter had increased. Increasing runoff in winter may be partly due to increasing solid precipitation in winter, which warmed up the permafrost and inhibited soil freezing. The ratio of runoff decreased in autumn and increased in winter, which probably due to the summer monsoon weakened.