High and low of annual runoff is related to amount of annual runoff and its distribution in a year. The traditional annual runoff classification only takes into account of amount of annual runoff, and ignores the distribution of runoff in a year. In order to overcome the drawbacks of the traditional annual runoff classification methods, a new approach to runoff classification: Set pair analysis method (SPA), has been proposed in this paper. Both amount of runoff and its distribution in a year have been taken into account in the approach. The key of SPA method is to calculate the connective degree of the set pair which is constructed with the classification set of monthly runoff in a year and the standard set, A case study, the classification of annual runoff at a hydrological station of Jinsha River, has been researched. The results show that the presented method is concise and the results of classification are feasible.