The musk deer is one of the least studied species that distributes throughout an alpine ecosystem. The population of musk deer is declining because of anthropogenic pressure. Our study was conducted to understand the relationship between musk deer and their environments in the Khaptad National Park in western Nepal. We used a line transect survey to observe the pellet of the musk deer in the study site. Our study found that the pellet group of the musk deer was found higher in the forested environment followed by open grassland, trails, and edge. Musk deer preferred an altitudinal range between 2,400 m and 3,200 m. Our study did not find any signs of the musk deer below 2400 m and above 3200 m. We also found that the pellet group of the musk deer had been mostly associated with close distance to a water body; however, it was found far distance to the village. The presence of livestock and human pressure could have been the reason for the musk deer to avoid edge areas. Anthropogenic pressure should be reduced in the musk deer habitats for long-term musk deer conservation in Nepal.