Abstract: The habitat quality is directly related to the habitat suitability provided by land use/land cover types for biodiversity. Habitat quality is seriously threatened by human activities, especially agricultural development activities, cities, roads. In order to assess the habitat quality and degradation degree in the ecologically fragile areas of Northwest China, taking Gansu Province as an example, based on the high-resolution (30 m) land use/ land cover type data and various types of natural reserve data, habitat quality module in InVEST software was used to evaluate the habitat quality and degradation, and both spatial analysis and local Moran's I were used to identify the hot spots and cold spots of habitat quality and degradation. On this basis, the relationship between habitat quality and degradation and the hot spots and all kinds of natural protected areas were analyzed. The results showed that: 1) The habitat quality was gradually decreasing from south to north, while, the habitat degradation was gradually increasing from north to south in Gansu Province. In the south and east of Gansu Province, the habitat degradation was also high, due to the strong disturbance of human activities, even though the habitat quality generally presented well. The habitat quality and degradation depended mainly on the location and intensity of human activities. The combination of habitat quality and degradation can more truly represent the current level of habitat protection. 2) The hot spots of habitat quality accounted for 25.59% of the total land area of Gansu Province, and most distributed in the south of Gansu Province, indicating a consistent with the proportion of natural conservation areas in Gansu Province. Most areas showed better natural ecological conditions, due to there was not many areas of degradation in hot spots. A recommendation can be made during this time, to turn the biodiversity conservation into the most endangered sites in the future; 3) In all types of protected areas, the habitat degradation of National Park was the lowest, whereas, that of other protectedareas was the highest. The coverage area of hot spot in habitat quality was much higher than that of habitat degradation. The coverage rate of hot spot significantly varied in the different types of protected areas. The coverage rate of hot spot for habitat degradation was also the highest in the protected areas, while that for habitat quality dominated in other types of protected areas. A suggestion was made during this time that the strategy planning of nature reserve can be focused on other protected areas, in order to strengthen the ecological restoration in other nature reserve, and further to reduce the interference of human activities. The findings can offer the accurate implementation of biodiversity conservation strategies and ecosystem management decisions in the western China.