Abstract: The present invention discloses a hydrological model considering the uncertainty of a runoff production structure and a method for quantifying influence on a surface-subsurface hydrological process. The present invention quantifies the uncertainty of runoff production structures including a surface runoff structure, an interflow structure and a base flow structure by using parameters, and constructs a hydrological model considering the uncertainty of a runoff production structure by combining an added confluence module. Compared with an original hydrological model, the hydrological model has higher precision, which is capable to quantify the uncertainty of surface runoff, interflow and base flow of the runoff production structure and its impact on the surface-subsurface hydrological process, better improve precision of runoff simulation, and enhance understanding and cognition of the basic rule of a hydrological physical process.