Habitat is the basic condition for human beings to survive and live. Taking Huizhou Cultural and Ecological Reserve as the research direction, the evaluation system is constructed by selecting three indicators of social layer, economic layer, and natural ecological layer. The research team used the entropy weights-TOPSIS assessment methodology to analyze the Habitat Environment Indices (HEIs) in different regions and at different times of the year. Gray correlation methodology was used to identify key drivers of Habitat quality. Findings: First, rural human settlements show a trend of recovery after a decline in 2013. Second, Jixi County (0.550) was ranked first in the overall evaluation. It is also consistently in first place in year-to-year changes. Third, the spatial pattern shows that the southeastern region is of higher quality, while the northern region is relatively backward. Fourth, the social (S) and natural ecological (NCE) layers are the dominant influences on the quality of village settlements. The secondary factors are mainly the proportion of good days in a year (0.977), the number of rural households (0.974) and the area of green space in gardens (0.974). The study achieves the purpose of enhancing the adaptability of the rural environment in the Huizhou Cultural and Ecological Reserve and provides a reference for enhancing the adaptability of related protected areas.