Based on the sample entropy, this study analyzed the spatial distribution and dynamic change characteristics of the complexity of runoff series using long-term daily runoff data from the Yichang, Hankou, and Datong hydrological stations, which were determined to be the main hydrological control stations in the Yangtze River. The results showed that the complexity of runoff series showed obvious spatial differences and an increasing trend from upstream to downstream in the Yangtze River. There was a negative correlation relationship between the annual runoff and the sample entropy value at every station. The complexity of runoff series at the Yichang and Datong stations showed a continuous increasing trend, and an increasing trend after 2000 at the Hankou Station.