The conservation of World Natural Heritage Sites has become a global concern. The identification of priority conservation areas can preserve the value of heritage sites while promoting sustainable development, which is important for balancing the conservation and development of heritage sites. This paper proposes an integrated framework for the identification of priority conservation areas for natural heritage sites based on landscape ecological risks (LERs) and ecosystem services (ESs), taking the Bogda heritage site in Xinjiang, China as a case study. The innovative approach combined the natural and cultural elements of natural heritage sites and included the following steps: (1) the LER index, Integrated Valuation of Ecosystem Services and Tradeoffs (InVEST) model and questionnaire method were adopted to assess the LERs and ESs of Bogda heritage sites during 1990–2018; (2) ordered weighted averaging (OWA) was used to identify conservation priorities by weighing LERs and ESs; and (3) the optimal priority conservation area was determined by comparing the conservation efficiencies under different scenarios. The results revealed that the LER, carbon storage (CS), habitat quality (HQ), aesthetic value (AV), and recreational value (RV) showed significant spatiotemporal variation. The most suitable priority conservation area was located at the central forestlands and high-coverage grasslands, with conservation efficiencies of 1.16, 2.91, 1.96, 1.03, and 1.21 for LER, CS, HQ, AV, and RV, respectively. Our study demonstrated that integrating LERs and ESs is a comprehensive and effective approach to identifying conservation priorities for heritage sites. The results can provide decision support for the conservation of the Bogda heritage site and a methodological reference for identifying conservation priorities for natural heritage sites. Furthermore, this study is also an effective application of LERs and ESs in identifying priority conservation areas.