Understanding spatial heterogeneity, which is a dominant function in ecosystem biodiversity, can help to highlight the conservation value and importance of a given area. However, there are limited available methods to assess the spatial heterogeneity of biodiversity value. We chose the kernel area of the Changbaishan Ecological Function Zone as the study site and constructed an assessment model of biodiversity value based on the dominant species in an area with high species richness and environmental variables, by using Maxent. Based on the aggregation of the dominant species and results of the biodiversity assessment, we partitioned the study area as into three areas of high, medium, and normal biodiversity values. Our study showed that the area with a high biodiversity value occupied 42.9% of the total study area and was mainly located within the Changbaishan Reserve; and the areas with high and normal biodiversity values comprised the main range of the Changbaishan Reserve. The mean and largest patch sizes of high biodiversity value were much larger than those of the medium and normal biodiversity values, reflecting the integrity and low fragmentation level in the landscape pattern, suggesting the competent function and robust stability of ecosystem and biodiversity values in our study. Together, the patches of high biodiversity value in the reserve were also larger and more integrated than those outside the reserve, and the order of the mean size with sub-function areas of the reserve was as follows:kernel area > buffer area > experimental area. Among the environmental factors, vegetation was the most important for the biodiversity value, followed by the soil depth and elevation in the study area. Based on the needs of protecting the ecosystem integrity and eco-process connectivity, the south buffer zone of the reserve should be incorporated into kernel areas; the large area with high and medium biodiversity values should be managed for more efficient conservation; and western Changbaishan Mountain was the most fragmented area with high diversity values and should be the focus of future conservation and management efforts. Our study also indicated that this method was effective to examine the spatial heterogeneity of biodiversity by associating the presence of dominant species with environmental variables and could be applied to biodiversity studies in other ecological function areas to delineate ecological conservation redlines and effectively design national parks.