In order to solve the problem that the quantitative standard coefficient is only determined by subjective experience of investigators in annual runoff prediction based on set pair analysis(SPA), we present a prediction model based on SPA in association with calibration of quantitative standard coefficient Firstly, we calibrate quantitative standard coefficient. Then, we predict the runoff by using SPA. Yichang station in Yangtze River is taken as an example, and predicted data by this model are compared with those by empirical quantitative standard model. The results show that predicted data by the model presented is more accurate to reflect original sequence than those by other models.