This is the second paper about the study of biodiversity and biological indication of butterfly in Chongqing, the purpose of this article is to set up the indication on environmental health of butterfly and of the environmental monitoring evaluation system. Basing on the previously study of the diversity parameters of butterfly in different ecological function divisions, this article focus on the research of the similarity analysis of different fauna. It has been selected 22 different diversity parameters of butterfly and 5 major environmental factors. In order to probe the selection of the monitoring index, the species and groups of indictor and to establish the evaluation system of environment, we have been analyzed them by means of regression analysis and principal component analysis. The result shows that, when observing on the region class, the diversity and evenness index of the species, genera and families in the 22 parameters could be neglected; in the 5 main environmental factors, the influence of the population pressure (X₂₂) is more than the other four factors which respectively are the region ratio (X₁₈), the population density (X₁₉), the proportion of woodland (X₂₀) and the amount of land containing (X₂₁). From the analysis of the diversity parameters, there are 10 factors that can be chosen for evaluating the environmental health of the ecological function divisions of Chongqing, the parameters are correspondingly the number of species (X₁), the genera of butterfly (X₂), the number of families (X₃), the dominance index of species (X₉), the contribution rate of different levels of the species number (X₁₀-X₁₃), the population pressure (X₂₂) and the synthetical score of the four principal component values. We also select 24 species and 12 groups of butterfly to monitor the environment, to probe the evaluating method. By means of the method above, we would anticipate that an environmental monitoring and evaluating system of ecological function areas in Chongqing might be established. Basing on the analyzing above and the assessment of the environmental health condition of various function areas, it can be discovered that the environmental health state of the first ecological function area is extremely healthy; the fifth, the ninth, the tenth of the function region is healthy; the ecological function area of the second, the third, the sixth, the seventh, the fourteenth is sub-healthy area; the healthy condition of the fourth, the eighth, the eleventh, the twelfth and thirteenth function region is unhealthy. However, the thirteenth and the fourteenth ecological function areas are urbanization areas, and the scores of both of them are not the lowest, this indicates that the relations of the urbanization and the environmental quality are incompletion causal relationship, it also recommends that the environmental of the cities and towns could be improved well through greening and environment protection. It can be expected that the monitoring and evaluating system could be further perfection in practice.