The correlation of wet and dry year of runoff between the water-exporting and water-importing area of western route south-to-north water transfer project was analyzed by SPA ,with description of identical, discrepancy and contrary to wet, normal and dry year. The results showed the connected structure is reasonable between sets and more than ten years’ cycle and quqsi-3 years cycle of runoff exist in the water-exporting and water-importing area . Each hydrological station among water-exporting and water-importing area keeped close correlation with wet, normal and dry year respectively. Adjustment reservoirs will be laid out in somewhere of water-exporting and water-importing area in order to rationally reserve abundant water and reduce unfavorable impact on lower reaches of the water-exporting rivers. Set Pair Analysis ( SPA) is an effective and new way to deal with the uncertainty problem.