[Obejective] The risks of secondary disasters and its impact on nature reserves and natural heritages in Jiuzhaigou earthquake area were studied in order to provide references for post-disaster recovery and reconstruction planning, as well as for nature reserves and natural heritages protection.[Methods] Based on land use data, DEM data, vegetation cover and natural protected area and heritage data, the spatial characteristics of ecological environment in Jiuzhaigou earthquake area were analyzed and the risk level of secondary disasters was assessed. Then, the risks of secondary disasters in nature reserves and natural heritage in earthquake area was assessed.[Results] The high earthquake intensity area was mainly located in the areas over 3 000 m altitude, where the land use was dominated by forest and grassland, and the mean vegetation coverage was up to 58%. The total area of high-risk zone accounted for about 30% of the study area, which mainly near to the fault zone and steeper slope zone. Nature reserves located in the central and south of the area, and most natural heritages located in high-risk zone, while the west and north regions were low-risk zone. To some extent, the secondary disasters aggravated the ecological risk of Jiuzhaigou scenic area and natural heritage.[Conclusion] The natural heritage areas, forest and grass and animal habitats were damaged by the earthquake with varying degrees, which had a serious impact on tourism in Jiuzhaigou scenic area. Therefore, Jiuzhaigou scenic area and Jiuzhaigou natural heritage should be the priority areas of restoration and reconstruction, and strengthen ecological protection and risk prevention.