Due to extensive poaching and habitat degradation, the Chinese pangolin (Manis pentadactyla) population had plummeted by approximately 90%, leading the International Union for Conservation of Nature (IUCN) to classify it as a Critically Endangered (CR) species. The scarcity of up-to-date data on the species’ distribution and dynamics presented a significant challenge in developing effective conservation strategies and implementing protective measures within China. This study employed on eleven widely used modeling techniques created within the BIOMOD2 framework to predict suitable habitats for the pangolin at the county scale, while examining the correlation between environmental variables and pangolin distribution. The results revealed that in Mingxi County, situated in the eastern sector of the Wuyi Mountains, the moderately suitable habitat spanned 260 km², accounting for 15% of the total area, whereas the highly suitable habitat encompassed only 49 km², constituting 3% of the total area. Within the county-managed nature reserve, the proportion of highly suitable habitats reached as high as 52%. However, nearly half of these areas, both moderately and highly suitable, remained inadequately addressed and conserved. The findings underscored the inadequacy of existing protected areas in sustaining the current pangolin population, leading to the identification of nine administrative villages that necessitated prioritized conservation efforts. The study anticipated an overall expansion in suitable habitats over the ensuing two decades, likely associated with an increase in precipitation, with significant growth projected in the eastern regions of Xiayang Township and Hufang Town. This research offered a clear and applicable research paradigm for the specific administrative level at which China operates, particularly pertinent to county-level jurisdictions with established nature reserve. In order to more precisely evaluate the pangolin’s situation at the county scale, the study underscored the paramount importance of conducting field surveys, deemed as the most urgent task at the time.