Loss of biodiversity due to the insufficient conservation of resources caused by land use is a serious problem humankind is facing. It is important to determine the priorities of biodiversity conservation. Based on the construction of an identification framework for a priority biodiversity conservation area, Xingguo County, a typical county administrative unit in the southern forested area of China, is used as an example. First, this paper constructs the priority identification framework for regional biodiversity conservation based on MCDA methods. Second, it adopts the InVEST-habitat quality model to evaluate the habitat quality in 2015. Third, factors such as elevation, slope, distance to nearest road and revenue loss for the forestry industry are selected to reflect the transportation cost, infrastructure cost, and opportunity cost of biodiversity conservation in the study area. By spatializing these factors and assigning weights to them, a spatial pattern of the biodiversity conservation costs in the study area is constructed. Last, a priority biodiversity conservation area is determined by an overlaid habitat quality map and the spatial pattern of conservation costs. The first priority area covers 620.61 km2, accounting for 19.31% of the total area of Xingguo County. Through well-financed biodiversity measures, the second and third priority areas can be selected using a stepwise approach. Our study may provide ideas and technical methods to help underdeveloped areas to achieve effective protection of biodiversity.