In order to ascertain impacts of Gezhouba Reservoir on the complexity of the Yangtze River system, multi-scale entropy theory was applied to analyze the runoff series of main stream of Yangtze River at the three main hydrological stations, which are Yichang, Hankou and Datong. The results show that the complexity of the runoff series of main stream of Yangtze River show increasing trend from upstream to downstream; Gezhouba Reservoir has certain impact on the complexity of the runoff series of main stream of Yangtze River. It changes the level of the complexity of the system under natural conditions, which decreases with the distance getting further.