The invention belongs to the field of health care food, and especially relates to a composition used for improving skeletal system health, and applications thereof. The composition comprises skimmed milk powder, fructo-oligosaccharide, yak bone, orange fruit powder, D-glucosamine hydrochloride, bone collagen, chondroitin sulfate, herba epimedii extract, rhizoma drynariae extract, mushroom powder, magnesium carbonate, casein phosphopeptide, and vitamin K2. The composition possesses excellent prevention effects on patients with osteoporosis and skeletal system disorders such as ankylosis, arthritis, osteoproliferation, arthralgia, and myospasm, and is capable of increasing bone mineral density, and improving skeletal system health. The composition can be used for preparing health care food capable of improving skeletal system health; application range is wide; and economic benefit and social benefit are both high.