The partition of surface runoff and infiltration is crucial in hydrologic modeling. To improve the flood prediction, we designed four strategies to explore the influences of the runoff partition method on the flexible hybrid runoff generation model. The runoff partition strategies consist of a hydrological model without the runoff partition module, a two-source runoff partition method, an improved two-source runoff partition method considering the heterogeneity of the subsurface topography and land cover, and a three-source runoff partition method. The Xin’anjiang hydrological model was used as the modeling framework to simulate a six-hourly stream flow for the Xun River watershed in Shaanxi Province, China. And the saturation-excess runoff generation and infiltration-excess runoff generation mechanisms were combined to construct the flexible hybrid runoff generation model. The performances of the four strategies were compared and analyzed based on the continuous flow discharge as well as the flood events. The runoff components analysis method was used to test the model’s conformity with the reality of the watershed. The results showed that the three-source runoff partition method was not applicable to the flexible hybrid runoff generation model because it overestimated the surface runoff and almost ignored the subsurface stormflow runoff. The improved two-source runoff partition method outperformed the others as it considered the heterogeneity of the watershed.