Storm runoff in basins is comprised of various runoff processes with widely disparate infiltration and storage capacities, such as Hortonian overland flow (HOF), saturated overland flow (SOF), sub-surface flow (SSF), and deep percolation (DP). Areas may be classified according to these various runoff processes based on the soil characteristics, geology, topography, and land-use. This study analyzes changes in runoff components in the Jialu River basin and the Fen River (Jingle sub-basin) during runoff generation from 1980 to 2013 using the runoff segmentation method. Based on the decision scheme, the dominant runoff process (DRP) in the basins was distinguished using geographic information system (GIS) tools. The impact of different runoff process distributions on the changes in the runoff for the basin was determined. The results show that the floods in the Jialu River basin and Jingle sub-basin were dominated by overland flow components. Compared with 1980–1999, the proportion of overland flow components for 2000–2013 in two basins showed a decreasing trend by 8.3% and 7.1%, respectively, while the interflow and underground runoff components increased. In addition, HOF was the DRP in the Jialu River basin and Jingle sub-basin from 2000 to 2013. The area of the rapid runoff processes (HOF, SOF1, and SSF1) in the Jialu River basin and Jingle sub-basin accounted for 89% and 78% of the entire basin, respectively. In contrast, the slow runoff processes (SOF2, SSF2, and DP) accounted for 11% and 22% of the entire basin, respectively. The runoff of the Jingle sub-basin was substantially lower than that of the Jialu River basin under the same rainfall conditions, because of the influence of the distribution of different runoff processes. Compared with the Jialu River Basin, the peak discharge and runoff of Jingle sub-basin were 190.4 m3/s and 2.85 mm lower on average, respectively. The results of this study provide useful information to understand land-use changes and formulate management practices to reduce flooding in the Yellow River.