The present invention provides a benzofuran compound, a preparation method and applications thereof, wherein the structure is represented by a general formula (I-1) or (I-2), R1, R3 and R4 are any one selected from hydrogen, C1-C5 straight or branched chain alkyl, hydroxyl, an aldehyde group, an acetyl group, a carboxyl group, a cyano group, an amino group, a nitro group, fluorine, chlorine, bromine, an amide group, an ester group, an alkoxy group, an aromatic group, and a heteroaromatic group, R2 is any one selected from hydrogen, C1-C5 straight or branched chain alkyl group, a hydroxyl group, an aromatic group, and a heteroaromatic group, and m and n are integers of 0-5. According to the present invention, the Staphylococcus aureus protease Sortase A substrate polypeptide fragment -LPXTG- is adopted as the structural simulation object, the benzofuran structure is adopted as the simulation substrate proline, and the linked amide hydrophobic fragment segment is used to stimulate the substrate leucine residue to design the novel protease Sortase A inhibitor.