At the 37th World Heritage conference in 2013, Xinjiang Tianshan successfully applied for World Natural Heritage. Xinjiang Tianshan has world-class aesthetic value and ecological value. However, with the continuous development and utilization of tourism resources, the ecological environment here is inevitably disturbed by human activities. It is a key problem how to accurately diagnose where the ecological environment has been damaged when we planning and managing natural heritage sites. To solve this problem, we need to build a landscape health diagnosis system based on RS and GIS technology and landscape ecology theory. This paper selects the Xinjiang Tianshan Natural Heritage Site Karajun-Kurdening region as the research area. Based on Landsat and sentinel-2 remote sensing images of 1977, 1990, 1997, 2013 and 2017, the ecological landscape of the study area was classified and interpreted by using the method of supervised classification. The landscape pattern index was calculated by fragstast software, combining landscape ecology theory and Chinese scholars' research results from the landscape stress degree, landscape vitality, natural heritage sites outstanding universal value, and landscape resilience 4 aspects. We constructed a landscape health diagnosis system suitable for mountainous natural heritage sites in arid regions using regional grid analysis and spatial interpolation method. The landscape health in Xinjiang Tianshan Natural Heritage Site Karajun-Kurdening region was diagnosed. In July, 2018, we carried out 17 aerial photogrammetry in the research area using unmanned aerial vehicle (UAV) to verify the accuracy of landscape health diagnosis system. Then, we used the Smart3D software to get 17 high-resolution orthophoto images, through comparing the orthophoto image with diagnostic image. The research results can be obtained. 1)In the past 40 years, the landscape of ice, water and theropencedrymion decreased seriously. The annual change rate of bare land obvious expansion was as high as 62.54%. 2) The landscape health status of the study area was average except in 1997. Since 1997, the landscape health value in the study area has been continuously increasing. 3) From 1977-2017, the landscape health in the north is better than that in the south of the study area. At the same time, the scattered distribution areas with poor or extremely poor landscape health status should be regarded as the key objects and typical areas of future protection work. It is worth mentioning that our landscape health diagnosis system has stronger applicability, landscape health diagnosis system can better monitor and diagnose the landscape health condition in the study area.