Abstract: Habitat destruction is an essential reason for the decline of the Yangtze finless porpoise (Neophocaena asiaeorientalis), a critically endangered cetacean species living in the middle and lower reaches of the Yangtze River. As the most fundamental measure for animal conservation, 8 nature reserves have been established since 1990s. However, due to the rush planning and establishment for protecting the key habitats, most of the reserves lack scientific evaluation for functional zoning. With the growing contradictions between economic development and ecological conservation, it is not easy to efficiently manage nature reserves under current regulations. Optimization and adjustment are urgently needed. Based on national policies, habitat preference of the Yangtze finless porpoise, and major economic development needs such as shipping, this study proposed principles and the following adjustment suggestions for the Yangtze finless porpoise nature reserves: (1) Divide the near-bank waters, river beaches, wetlands, and bifurcated tributaries, which the Yangtze finless porpoise preferred, into the core protected area. (2) Divide the main channel waters and the region between the Yangtze River dike and the core protected area boundary into the general control area. (3) Consider the history issues, refine the management statement in different areas. The above adjustment suggestions make the functional zoning more consistent with the distribution characteristics and habitat preference of the Yangtze finless porpoise, and more efficiently protect their natural population and habitat. Also, it could straighten the legal contradictions existing on the management level of nature reserves, which will make the management more targeted and operable, and provide a practical, feasible model for the healthy development of Yangtze finless porpoise nature reserves.