Correlation among indexes is an ineluctable problem in comprehensive evaluation. On the basis of the research at home and abroad, two methods of correlation analysis, i.e. quantitative analysis and qualitative analysis were proposed to analyse their scopes of application. As an example, the correlation analysis was applied to the analysis of indexes of healthy Yangtze River assessment. The result shows that indexes of the first class are generally independent, but indexes among the second class and some of them with first class indexes are correlative strongly. It is demonstrated that the correlation analysis and elimination on indexes must be emphasized in the establishment of indexes system.