Alpine natural heritage sites hold significant value due to their unique global resources. Studying land cover changes in these areas is crucial for maintaining and preserving multiple their values. This study takes Kalajun-Kuerdening, one of the components of Xinjiang Tianshan World Natural Heritage Site, as an example to analyze land cover changes and their driving factors in alpine heritage sites. Highlights include: (1) Between 1994 and 2023, Forest and Grassland increased by 55.96 km2 and 18.16 km2, with notable forest growth from 2007 to 2017. Trends in Forest changes align with forest protection policies, and a substantial amount of Bareland converted to Grassland indicates an increase in vegetation cover. (2) Elevation, precipitation, temperature, and evapotranspiration are key drivers of land cover changes, as validated by Random Forest algorithm and Geodetector model. (3) Favorable conditions for Grassland to Forest transition include annual precipitation between 275 and 375 mm, annual temperature between −2 and 3 °C, annual evapotranspiration between 580 and 750 mm, elevation between 1800 and 2600 m, and aspect between 0 to 110° and 220 to 259.9°. Continuous monitoring of land cover changes and their driving factors in mountain heritage sites contributes to the protection of the ecological environment and provides data and information support for addressing climate change, resource management, and policy making.