Eupolyphaga sinensis Walker (ESW), an animal drug in traditional Chinese medicine, has been used clinically for thousands of years for cardiovascular disease and osteoarthritis. Many studies of ESW have reported that it had have anti-in ammatory and anti-tumor activities due to the small-molecule ingredients. However, large-molecule compounds of ESW representing signi cant pharmacological effects such as anti-thrombotic, anti-cancer, and anti-in ammatory have not been revealed yet. Here, a novel anticoagulant peptide (P9) containing 9 amino acids was isolated from the hydrolysate of aqueous extracts of ESW. Further, P9 synthesized by solid-phase synthesis was able to prolong APTT and TT and bind to thrombin in a mixed mode. Molecular docking and spectroscopy demonstrated that P9 was able to inhibit thrombin activity by binding to the active site of thrombin and altering the secondary structure of thrombin. In an in vivo study, P9 was able to reduce the intensity of Phenylhydrazine (PHZ)-induced cardiac staining in thrombosed zebra sh with antithrombotic activity. The results suggest that peptides originated from ESW hydrolysates could exert an anticoagulant effect, which is likely to be a potential source of bioactive peptides with anticoagulant activity.