Runoff variations contribute greatly to the scarcity of available water resources and the deterioration of eco environment system. In this paper, we analyzed the characteristics of runoff variations in Haihe River Basin during different periods using the combination of variable separation and Mann-Kendall test method, and discussed the contribution of each influencing factor quantitatively. The results indicate that the precipitation was the dominant factor of runoff variations in Haihe River Basin from 1956 to 2000, with the contribution rate of 80.8%. However, the dominant factor transformed from precipitation to land use change caused by human activities from 2001 to 2016. The contribution rate of climate change decreased to 29.0%, and that of the underlying surface rose to 71.0%. From the spatial distribution pattern, it showed that precipitation significantly affected the runoff variations of north Haihe River sub basin, south Haihe River sub basin and Tuhai-Majia River sub basin, and the individual contribution rate all exceeded 85%. Compared with other sub basins, Luan River sub basin was affected more severely by the underlying surface, with the contribution rate of 30.2%. The study of the runoff variations and their influences can provide valuable guidance for the protection of eco environment and the sustainable utilization of water resources in this area.