The feces of Alpine musk deer (Moschus chrysogaster) and Alashan red deer (Cervus alashanicus) were collected in the Helan Mountains, and their feeding habits in autumn were studied by microscopic analysis of the feces. The fecal samples and plant samples were collected from the habitats of Alpine musk deer and Alashan red deer, and 40 compound samples were obtained for each species. The autumn diet proportions of Alpine musk deer and Alashan red deer were processed using the frequency conversion method. The results showed that the diet of the Alpine musk deer consisted of 30 species of 20 families in autumn, including Lonicera edulis (11.96%), Astragalus spp. (10.17%), Salix characta (8.32%), Spiraea spp. (6.82%), and Leptodermis ordosica (6.18%). The diet of the Alashan red deer consisted of 29 species of 12 families, including Stipa spp. (22.15%), Ulmus glaucescens (21.14%), Poa spp. (16.90%), Potentilla parvifolia (11.62%), and Populus davidiana (10.00%). The Alpine musk deer and Alashan red deer shared nine species of food plants in total, and the index of niche overlap was 83.75%. The Shannon-Wiener index, Pielou uniformity index, food niche breadth index, and largest species diversity index were higher in Alpine musk deer than in Alashan red deer.