Taking the 12 representative rural rivers of Yancheng City as examples, the relationship between the ecosystem health and service function of rural river were analyzed, and the approaches of realizing the both in the rural river treatment were probed. The results show that there is a stress response mechanism between the service function and ecological health of the rural river, the contents and standards of river ecosystem health evaluation both reflect the influence of river service function. In view of internal hierarchy influence of river system, and many natural attributes of rural rivers, the authors of this paper think that the ecological restoration of rural rivers should rely on the self organization and self recovery ability of river system as far as possible, and the natural ecological functions of rivers should be remained or promoted during rural river treatment, and the overall upper layer elements and the river ecosystem health recovery should gradually promoted from the basic river morphology and such basic elements as hydrology and water power.