Grey relational analysis is one of the most important methods in water quality evaluation system. As the traditional grey relational analysis has the defects of homogenization in static resolution ratio, small discrimination in correlation degree, and low precision in the weight of impact factors, this paper proposed an advanced grey relational analysis that used dynamic resolution ratio and comprehensive evaluation indicators. This method has been applied in the MIS software which monitors and evaluates the water quality in the lakes of the Four-Lake Basin. Compared with the traditional grey relational analysis and the cluster-factor analysis, this method could effectively enhance the reliability and accuracy of the results.