In terms of habitat conservation, it is essential to develop a habitat assessment system that can evaluate not only the suitability of the current habitat, but also the health and stability of the habitat. This study aimed to develop a methodology of habitat quality assessment for endangered species by analyzing various existing habitat assessment methods. The habitat quality assessment consisted of selecting targeted species, planning of assessment, selecting targeted sites, assessing performance, calculating grade, and expert verification. Target sites were selected separately from core and potential habitats using a species distribution model or habitat suitability index. Habitat assessment factors were classified into ecological characteristic, landscape characteristic, and species-habitat characteristic. Ecological characteristic consisted of thirteen factors related to health of tree, vegetation, and soil. Landscape characteristic consisted of five factors related to fragment and connectivity of habitat. Species-habitat characteristic consisted of factors for evaluating habitat suitability depending on target species. Since meanings are different depending on characteristics, habitat quality assessment of this study could be used by classifying results for each characteristic according to various assessment purposes, such as designation of alternative habitats, assessment of restoration project, and protected area valuation for endangered species. Forest habitat quality assessment is expected to play an important role in conservation acts of endangered species in the future through continuous supplementation of this system in regard to quantitative assessment criteria and weighting for each factor with an influence.