The present invention provides a low-molecular-weight heparin sustained-release preparation, a preparation method and application thereof, wherein the low-molecular-weight heparin sustained-release preparation comprises nanoparticles formed by polypeptides and low molecular weight heparin, and the polypeptides are cross-linked through chemical bonds. The present invention adopts any one or a combination of at least two of self-assembly technology, freeze-drying technology, homogenization technology, emulsification technology, embedding technology or spray-drying technology to prepare low molecular weight heparin sustained-release preparation. The low-molecular-weight heparin sustained-release preparation of the invention has a release rate of only about 20% within 500 hours under in vitro conditions, has a sustained-release effect, can effectively prolong its blood half-life, avoid the "peak-to-valley fluctuation" of the drug, and reduce the dosage of the low-molecular-weight heparin solution. The risk of hemorrhage when the dose is used, the toxic and side effects of the drug are reduced, the compliance of patients is improved, and the treatment efficiency of the disease is improved, and can be used for the prevention and treatment of thrombosis diseases. The preparation method of the invention is simple and has broad application prospects.