In order to comprehensively renovate the ecological environment of Fen River basin, according to the water ecological monitoring data of Fen River in 2016, the candidate index system of ecosystem health was constructed from the water physical chemistry and aquatic biological characteristics aspects. The principal component analysis and correlation analysis method were adopted to screen evaluation indicators, and the river health evaluation index system of 15 indexes was obtained, which incorporated the benthic animal diversity index, fish diversity index, petroleum , dissolved oxygen, nitrate nitrogen, COD, BOD, total nitrogen, total phosphorus, fluoride, anionic surfactant, zinc, chromium, copper and cadmium. The improved grey correlation degree method was then used to evaluate the health of river ecosystem and the river health grade under the conditions of multiple indicators. The results showed that in 37 sampling points of the upper and middle reaches of Fen River, the number of the "healthy" level was 12 and the "sub-healthy" level was 1, accounting for 35%. The "ordinary " level was 7, accounting for 19%, and the other 46% was classified as the "sub-sick" and "sick" level. The health and sub-health level sampling points were located in the north of the upper and middle reaches of Fen River, which was less affected by human activities, while the sub-sick and the sick grades were mainly located in the south. The domestic sewage, industry and animal husbandry industry pollution were the main causes of river pollution.