A method for dividing watershed by grid inlaid in watershed basic unit is discussed. As big data can precisely describe space distribution of rainfall and spatial variability of underlying surface, a calculation method based on big data, considering effects of space distribution of rainfall and spatial variability of underlying surface on runoff yield and confluence, is proposed. Through an introduction of “grid drop”, the physical nature of watershed instantaneous unit hydrograph is revealed, and the theory of geomorphologic instantaneous unit hydrograph by Rodriguez-Iturbe and Valdes is supplemented. In addition, the limitations of the isochronism line method and the unit hydrograph method are investigated. It can be concluded that the proposed theory of runoff yield and confluence by grid inlaid overcomes the disadvantage and assimilates the advantages of the two methods mentioned above, and provides a possibility of unifying the two methods.