The uncoordinated relationship between runoff and sediment has become a key problem restricting the high-quality development of the Yellow River. Revealing the main influencing factors of changes in runoff and sediment transport has guiding significance for soil erosion control under the conditions of ecological and economic development. This study took the Ru River Basin as the research object. The M-K test and Pettitt test were used to analyze the water and sediment change trend of the Ru River Basin from 1989 to 2019. The contribution rate of human activities to the changes of runoff and sediment transport in the Ru River Basin was quantitatively studied by using the double mass curve method. The main influencing factors of runoff and sediment transport change were explored by random forest regression analysis. The results show that:(1) the runoff and sediment transport peak corresponded well in the Ru River Basin, but the runoff and sediment transport showed obvious differences after 2012, with the runoff increasing gradually and the sediment transport decreasing steadily. (2) The sudden change of runoff in the Ru River Basin was in 1996 and 2003, and the sudden change of sediment transport was in 1996 and 2004. In the two stages of the impact period, the contribution rates of human activities to runoff were 95.95%and 77.52%, respectively, while the contribution rates to sediment transport were 78.31% and 77.91%, respectively. (3) The factors that significantly affected the runoff were crop sown area, the cultivated land area, grassland area and population density. The factors that significantly affected sediment transport were vegetation coverage, proportion of water conservancy and environmental investment, population density and total industrial output value. (4) The influence of crop sown area and cultivated land area on runoff was significantly positively correlated. There was significantly negative correlation between grassland area and population density in response to runoff. Factors such as vegetation coverage, proportion of water conservancy and environmental investment, and total industrial output value had significantly negative correlation with sediment transport. The influence of human activities on runoff and sediment transport change was complex and changeable, and the effect on runoff and sediment transport was easily limited only in the case of single factor. At present, the control of soil and water loss needs to be integrated with economic, ecological and social factors.