Taking the upper and middle reaches of the Huaihe River (above Bengbu Station) as the study area, seven flow indicators including the high flow, average flow and low flow are adopted to characterize the features of runoff changes and investigate the influences of climate change and human activities on the runoff characteristics at different time scales. Firstly, the Mann-Kendall trend test and the sliding Ttest are used to identify the mutation year of each flow index. Secondly, the derived differential equation of flow indicators change is used to improve the original method based on the Budyko hypothesis, so as to quantitatively identify the contribution rate of climate change and human activities to the change of runoff. Finally, the driving mechanism of human activities on changes of runoff characteristics is analyzed by constructing a land-use transfer matrix. The results show that most of the flow indicators in the upper and middle reaches of the Huaihe River show a downward trend after mutation years. Among them, the average flow indicators declined most significantly, ranging from 2.25% to 44.25%. High flow indicators, floodseason runoff depth and climate indicators have the highest correlation, with a correlation coefficient of 0.859~0.987, while low flow indicators and non-flood season runoff depth have a low correlation. Climate change and human activities make most of the flow indicators show a downward trend, among which human activities are the dominant factor, and their contribution rates at Xixian, Wangjiaba, Lutaizi, and Bengbu stations are from 87.55% to 98.46%, 80.91% to 88.50%, 80.42% to 92.42% and 83.23% to 99.99%, respectively.