The invention discloses an endangered wildlife habitat suitability distinguishing method based on a GIS. The endangered wildlife habitat suitability distinguishing method includes the steps of firstly, determining the endangered wildlife required to be studied in a nature protection area, researching the nature and humanity conditions of the nature protection area and the life habits of the endangered wildlife, then carrying out outdoor data collection and space data compilation, selecting the nature factors and the human factors having great influences on the endangered wildlife, being free of the need to obtain the area where the endangered wildlife moves and appears in advance, building an ecological niche model based on the GIS, quantizing the habitat suitability, and dividing the habitat into the high-suitability habitat, the middle-suitability habitat, the low-suitability habitat and a non-suitability area. According to the endangered wildlife habitat suitability distinguishing method based on the GIS, wide-range suitable endangered wildlife habitat distinguishing can be achieved, limited manpower and material resources can be developed to the greatest degree, and therefore the wildlife habitat protection efficiency and the wildlife habitat protection benefits are improved. The method for calculating the wildlife habitat suitability is disclosed, the area which is required to be preferentially protected in the nature protection area can be visually reflected, and building, construction and management on the nature protection area are guided.