The idea of stochastic differential was applied to the process of river runoff in this paper.Considering the uncertain of the process of river runoff,the paper set up the model of stochastic differential equation and simulated outflow process of the river,and then certified the model by measured data of a hydrology station in this river. The result showed that statistical parameters of calculating value are better accordant with that of measured value and the accuracy and pricision of the model is high.The model has higher feasible in application of regulating flood calculation.This paper can provide a new idea for flood checking computation of river and scientific basis for uncertain flood computation considering the process of flood checking computation of river.