Abstract: The aim for this research is to select suitable methods to assess the health of the river ecosystem of rivers flowing through urban areas. Based on the water quality, river habitat, phytoplankton and benthic invertebrate data collected from the Chengdu section of the Min River, the number of total taxa, Trichoptera taxa, and Ephemeroptera taxa, and the percentage of EPT taxa, dominant species, and Diptera taxa were used to formulate a benthic index of biotic integrity (B-IBI) system. The B-IBI was used to assess the health state of the Min River in Chengdu section, and the results were compared with that using water eco-environment quality index (WQI). The results showed 5 healthy state sites, including one sub-healthy state site, five fair state sites, two poor state sites, and 10 extremely poor state sites. The comparison of results based on the two methods indicated that the results of both methods were comparable for the same sites. B-IBI can fully describe biological integrity. The health assessment results of different cities revealed a healthier river ecosystem in the upstream than in populated and developed downstream areas. The study showed that the B-IBI is suitable for the health assessment of the Min River in Chengdu.