According to the suvery on benthic animal and fish samples, and combining with monitoring data, we analyzed the health condition of aquatic ecosystem, and made evaluation with an index in Aojiang Basin. The results showed that the water quality was generally good in Aojiang Basin, but total nitrogen and total phosphorus concentration of Shanzi Reservoir exceeded standard for a long term which led to ecological environment problems, such as eutrophication and algae outbreak. Species numbers of benthic animals presented in the tributaries were greater than that in the river, with smallest species number in reservoir. The fish composition in the upstream, midstream and downstream was not of significant difference, exhibiting a tropical and subtropical floristic characteristics. The health condition of aquatic ecosystem in both upstream and midstream was good, while that in downstream was moderate.