The protection of World Natural Heritage Sites (WNHSs) has become a global undertaking, wherein Outstanding Universal Value (OUV) is an important aspect of heritage protection. Focusing on the protection of the aesthetic and bioecological values of Bogda (one component of Xinjiang Tianshan WNHS), 17 indicators are selected to construct a Heritage Value Protection Significance Index (HVPSI) and a related Heritage Value Protection Index (HVI). From these, the level of OUV conservation is obtained according to the five aspects of integrity, vulnerability, sensitivity, degree of human impact and environmental factors. The spatial autocorrelation analysis method was applied to the OUV conservation indices to comprehensively reflect the spatial-pattern characteristics of the heritage value in the study area. According to the spatial-division of the HVPSI, the plant community composition and diversity characteristics of different HVPSI zones are analyzed by a field survey (July 2018 and 2019). To verify the rationality of space partition and identify the OUV elements in each HVPSI district, a spatial-econometric model is then used to explore the relationship among HVPSI, HVI and community diversity. This study provides a scientific basis for management of heritage sites and a theoretical basis for further investigation into heritage site indicators.