Abstract: In this paper, Guzhushan Nature Reserve was taken as the research object, and the fauna and flora in the reserve were investigated using the method of sample plot survey and line transect survey, referring to the ecological evaluation indexes of wild plant type nature reserve in the Technical Regulations for Evaluation of Natural Ecological Quality of Nature Reserve (LY/T1813—2009). The ecological quality of the protected area was evaluated by analytic hierarchy process based on the influence factors of typicality, rarity, naturalness, suitability of area, vulnerability and intensity of human activities. After the evaluation and analysis of the influence factors of species typicality, species endangerment degree and regional distribution, habitat condition, naturalness, ecosystem stability, resource development and utilization, the scores of each sub-index are low, and the evaluation score is 37.7, indicating that the ecological quality of the nature reserve is poor. The overall situation of ecological quality in Guzhushan Nature Reserve is not optimistic. Although the protected species are strong, the ecological protection measures in the reserve are not in place, the overall stability of the ecosystem is not strong, and the development and utilization of resources and surrounding areas have potential threats to the natural resources.