Yancheng Nature Reserve in east China is of great importance to the protection of biodiversity. It is a principal refuge for Red-crowned Cranes (Grus japonensis) and many other rare species, an important station for migrant waterfowls in the Asian Pacific, and a captive breeding base for Milu (Elaphurus davidianus). However, since the late 1980s, serious losses of biodiversity have been emerging in the protected area. In this study, to value objectively and improve management of the Yancheng Nature eserve, a new approach for conservation management is proposed by virtue of the theories of selforganizing systems, functional group classification and target species selection. According to this approach, biological components in Yancheng Nature Reserve are classified into 10 supporting functional groups, eight target functional groups and 11 subordinate functional groups. Eight target species were selected from those target functional groups, i.e., G. japonensis, E. davidianus, Hydropotes inermis, Larus saundersi, Centropus toulou, Felis bengalensis, Paradoxornis heudei, and Platalea minor. Past observations in Yancheng Nature Reserve illustrate that the new approach is feasible, and this new approach will also benefit the management of the nature reserve.