Moschus chrysogaster is endemic to China, and now its number is less than one hundred in Helan Mountain. Habitat suitability assessment of Moschus chrysogaster in Helan Mountain is the premise and basis for protecting and restoring the population of Moschus chrysogaster in Helan Mountain. 750 occurrence points of Moschus chrysogaster were confirmed by using the line transect method. Combining 13 kinds of environmental factors, the MAXENT model was used to determine the main factors affecting the distribution of Moschus chrysogaster, and to assess its potentially suitable habitat in Helan Mountain. The distribution map of suitable habitat and unsuitable habitat of Moschus chrysogaster could be obtained according to the Jorden index. The results showed that the coniferous forest, the distance from water source, the distance from forest ridge, altitude, the distance from mining area and the distance from road were the most important environmental factors affecting the suitable habitat distribution of Moschus chrysogaster. The suitable habitat of Moschus chrysogaster was mainly distributed in the central part of Helan Mountain. The suitable habitat area covered 120.24 km², which accounted for 3.27% of the total area, and the unsuitable habitat area was 3555.72 km². The results showed that the AUC (the area under the receiver operating characteristic curve) value was 0.992, suggesting perfectly predictive effect of the model. It is suggested that the management organizations should strictly control the human disturbance, identify and establish ecological corridors between suitable habitats, and attach the importance to the use of scattered potentially suitable habitat of Moschus chrysogaster to ensure the development of this population.