Based on analysis of runoff variation trend, climate background in the Fenhe watershed since 1970s, the relationship among temperature, precipitation and runoff, the climate change on characteristics since the mid-1980s, the natural annual runoff computational formula was established for the Hejin station, the effect of climatic change on runoff was discussed. The results showed that:(1) There was obvious decline in runoff after the high-water periods in 1950s or 1960s; (2) River exhaustion and zero flow in the Fenhe River since 1970s were taken as the background of the heating effect in northern hemisphere; (3) Compared with earlier the raising temperatures in winter, and what the most, the reduce precipitation especially during flood season, or summer and autumn, were most significant; (4)The reduce amount of runoff, which was caused by the climatic change, was 567million m3/a(24.9%), of which the temperature influence was about 8.6%, rainfall influence was about 16.3%. Therefore, the climate change and its effect on runoff in Fenhe Watershed were significant.