The invention relates to the field of biomedicine, and discloses a synthetic polypeptide BNC (basal nucleus complex) with antithrombotic activity, a preparation method thereof and an application of the synthetic polypeptide BNC as an antithrombotic agent. The BNC is synthesized by using a Fomc solid-phase chemical process, and contains 3 amino acid residues; the sequence of the BNC is Pyr-Asn-Cys; the molecular weight of the BNC is 346; and the structural formula is shown in the specification. The animal experiment indicates that the polypeptide has inhibiting effects on the formation of thrombus after electrically stimulating the common carotid artery intima of a rat and the formation of ADP-induced (adenosine diphosphate-induced) acute lung thrombus of a mouse, and can prolong the coagulation time of the mouse. The structure formula of the BNC is shown in the specification.