With the enlargement of water quality monitoring scope and network, traditional methods of water quality indexes correlation analysiscan no longer be applicable to a large amount of water quality data. But the cluster analysis method can work it. SPSS software was used to calculatethe correlation coefficient matrix of water quality index with cluster analysis method. And a tree diagram was drawn to analyze the correlation ofwater quality data. It is concluded that the total organic carbon and potassium permanganate index, total nitrogen and ammonia nitrogen have strongcorrelation. Combined with the verification of linear regression, it can be proved that the R cluster analysis has a good effect on the study of waterquality index correlation, and it can play an important role in water pollution control or water quality monitoring and evaluation.