Studying the change characteristics of the runoff complexity in the upper reaches of the Yellow River has great significance to the understanding of regional runoff evolution. Here, both flexible sample entropy and multiscale entropy were used to measure the annual, flood and non flood season runoff complexity of 12 hydrological stations located in the main stream and tributaries of this region from 1956 to 2015, based on which the change characteristics of runoff complexity under different time scales was analyzed. The results showed that the annual runoff of the upper reaches of the Yellow River showed an insignificant downward trend, and the runoff decreased during the flood season but increased during the non flood season. Except for the Minhe Station of Huangshui River, all the other stations in the tributaries showed a significant downward trend in runoff including annual, flood season and non flood season runoff. Under different time scales, the runoff complexity of annual, flood and non flood season from Guide Station to Lanzhou Station in the main stream was greatly differentiated from that of Minhe Station of Huangshui River in the upper reaches of the Yellow River. The changes in runoff complexity also reflected the impacts of human activities. On a single time scale, the impacts of human activities on annual and non flood season runoff were stronger than that on flood season runoff, whereas on multiple time scales, it was the opposite. But, regarding to Minhe Station of Huangshui River, the impacts of human activities varied significantly at different time scales and different periods. Using the flexible sample entropy and multiscale entropy at the same time can help obtain detailed runoff complexity change characteristics, and identify the intensity difference of the impacts of the human activities. The recharge ratio of base flow to annual runoff and non flood season runoff in the upper reaches of the Yellow River was higher than that of the whole basin, and the change of base flow had a significat impact on annual runoff.