Based on historical records from two hydrological stations of Wangdaohengta and Wenjiachuan, the runoff variation characteristics and influence factors, which include runoff inter-annual variation characteristics, changing trend, precipitation change, and the impact of human activities, were analyzed by using different analyzing methods, such as Mann-Kendall trend analysis, R/S analysis, and double mass curve for annual rainfall stream flow. The results showed that the multi-year change of runoff had a distinctive decreased tendency, especially since the end of the 20th Century. The Hurst index were 0.853 and 0.803 for the Wangdaohengta and Wenjiachuan stations, respectively, which indicates that the decreasing trends of runoff in Kuye River would continue in the future.The rainfall and human activities had a different influence on runoff in different periods. During 1997-2010, the runoff descending proportions caused by the human activities are as high as 80.48% and 93.62% in Wangdaohengta and Wenjiachuan stations, therefor aggravating human activities were the main reason for runoff descending in Kuye River.