Distinguishing the effects of climate change and land use change in a river basin on its runoff is crucial to deep understanding of water resources formation and evolution, rational exploitation and utilization, and environment protection. This paper describes application of a conceptual eco-hydrological model, developed by Tomer using water balance and energy balance principles for separation of these effects in Shiyang River basin under climate change and human activities. The study area covers the sub-basins of five mountainous tributaries: Dajing river, Gulang river, Huangyang river, Zamu river and Jintai river. In recent years all the tributary runoff have took a decreasing tendency and showed a variation point. The results show that in the same drought period the influencing factors of different sub-basins were not the same, but climate change was the major factor for the runoff changes in all the five tributaries throughout the study period.