[Objectives] The Alpine Musk Deer (Moschus chrysogaster), belonging to the family Moschidae of the order Cetartiodactyla, is endemic to China and classified as a first-class animal under national protection. It primarily inhabits the Qinghai-Tibet Plateau and surrounding regions of China. The Yarlung Zangbo River Basin represents one of the critical distribution areas for the Alpine Musk Deer. Studying the habitat suitability and activity rhythms of this species in the Yarlung Zangbo River Basin can promote the conservation of Alpine Musk Deer populations and facilitate effective habitat management. [Methods] By resource surveys and infrared camera monitoring in the Yarlung Zangbo River Basin, we obtained a total of 51 distribution sites of the Alpine Musk Deer. Then, employing 22 environmental factors, including topography and climate, we constructed a MaxEnt model in MaxEnt 3.4.4 to assess the factors influencing the habitat selection of this species and map the current distribution of suitable habitats in Yarlung Zangbo River Basin with ArcGIS 10.8. Furthermore, we predicted the future distribution of suitable habitats under different climate scenarios to analyze the potential habitat change trends. Finally, we utilized infrared camera data to examine the species’ daily activity patterns with R 4.4.3. [Results] (1) The area under the receiver operating characteristic curve of the MaxEnt model was 0.926, indicating high accuracy of the prediction (Fig. 2). (2) The main environmental factors affecting the habitat selection of the Alpine Musk Deer in the Yarlung Zangbo River Basin were the precipitation of coldest quarter (Bio19) and aspect, with a total contribution of 89.3% (Fig. 3, Table 2). (3) Under current climatic conditions, the suitable habitats of the Alpine Musk Deer are mainly distributed in eastern Xigaze, central and southern Lhasa, northwestern Shannan, and western Nyingchi. The high suitable habitats are predominantly distributed along the border regions of Lhasa, Xigaze, and Shannan (Fig. 6). (4) The prediction under different future climate scenarios shows a reduction in high suitable habitat areas with the increase in temperature, alongside a more concentrated distribution pattern (Fig. 5). (5) The daily activity rhythm of the Alpine Musk Deer exhibited a distinct crepuscular pattern (Fig. 7). [Conclusion] The study can deepen our understanding of population dynamics of the species in the region and provide a theoretical basis for its conservation and habitat management in the future.