The Qilian Mountain Grassland is an important animal husbandry production base in northwestern China. Horses, cattle, and sheep are the main livestock, which are widely distributed in the desert grasslands and alpine meadows around the Qilian Mountains. Grazing livestock produce large amounts of feces, and the germinable seeds in feces constitute the seed banks. Research on the size, plant species composition, and distribution of livestock dung seed banks in the Qilian Mountain grasslands may help understand the interactions between grass species and livestock and inform the comprehensive management practices for grazing livestock. In mid-October 2018, we collected the dung of horses, cattle, and sheep in the alpine meadows and desert grasslands of the Qilian Mountains and estimated the composition and size of the dung seed bank by the greenhouse germination method. Seeds of aboveground vegetation in the same location were also collected to determine the relationships between the size and composition of dung seed banks and the seed traits (i.e., mass and shape). A total of 30 plant species germinated from the dung seed banks of the three livestock species, of which 22 species (73%) were perennial. The seedling densities for horse, cattle, and sheep dung were 11.91, 10.80, and 7.60 seedlings per gram dung, respectively. The species richness, species diversity, and Jaccard coefficients of similarity between dung seedling and aboveground vegetation of horse dung were significantly greater than that of cattle and sheep dung. Regression analyses indicated that medium-sized (10−30 mg) and spherical (0.04−0.10 shape index) seeds had the greatest germination potential. Our study suggests that, of the three livestock species tested, the horse dung seed bank contributes most to grassland recovery and restoration of the Qilian Mountains.