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In many river basins in China, flood and drought coexist. Therefore, there is a strong demand to rationally utilize the flood waters. Water resources compensation characteristics analysis is the foundation of utilization of flood. In this paper, set pair analysis, a new uncertainty analysis method, was used to analyze the dry and wet compensation characteristics of the water resources parameters in the Dongjiang River, including precipitation, monthly mean discharge of Heyuan, Lin gxia, Boluo gauges. The results showed that the dry and wet encountering chance of precipitation and monthly mean discharge were rather large, there was no compensation characteristics. The monthly mean discharge in some curtain had the synchronization characteristics with the precipitation in the area. At the same time, there exists some degree of difference and opposition characteristics, indicating that there were some conditions for flood utilization in the Dongjiang River basin. Furthermore, correlation coefficient, fuzzy membership and grey correlation degree were adopted to test the result of set pair analysis. The results showed that set pair analysis provided consistent information with the traditional analysis method. The study demonstrated that the set pair analysis was an efficient method in study of water resources compensation characteristics.