World Natural Heritage Site (WNHS) is a typical demonstration of global diversity protection. To realize the sustainable development of WNHSs under the contradiction of protection and utilization, an index system based on the framework of exposure- sensitivity- resilience was constructed to diagnose the ecological degradation of WNHSs, and the degree and structure of ecological degradation were evaluated and visualized in Bogda, Tianshan Mountains, Xinjiang. The results show that: (1) The criterion layers of threat factors, resilience and changes of heritage value showed different spatial distribution characteristics. (2) The level of ecological degradation in Bogda site was mainly mild degradation, while the degradation was serious around the scenic spots with intensive tourist activities and along the road. The seriously degraded area was the least, accounting for 1.89% of the study area, followed by ecological health area (6.22%), moderately degraded area (13.87%), and mildly degraded area (78.03%). (3) The overall conservation management status in Bogda site remained good. Low -low -low is the main type of ecological degradation, followed by high -high -high, high -high -low, low -high -high and low -high -high. The diagnosis and analysis of ecological degradation would provide scientific basis for the conservation, management and ecological restoration of Bogda site.