Analyses of animal species distribution in a neutral or minimally-interrupted habitat provide a baseline that is essential for assessment of population status, identification of key habitat, and conservation planning for habitat protection and restoration. In this study, we surveyed the occurrence of the Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) and corresponding habitat characteristics, including bathymetry, benthic slope and fish resources, in the newly established He-wang-miao reserve. Based on sightings from field surveys, the extent of occurrence of the finless porpoise was 9.532 km2. General linear model analysis indicated the distribution of the finless porpoise was influenced by water depth and fish density. Habitat preference analysis illustrated a proxy to identify key habitat for the finless porpoise: moderate water depth (between 7 m and 12 m), flat benthic slope (lower than 2°) and moderately-high fish density (0.6 ind/m3 and 1.2 ind/m3). We proposed that this proxy has great potential for conservation planning to identify habitat conservation priorities in the Yangtze River and to guide management actions such as ex situ reserve selection and habitat restoration.