The work aims to graft ε-polylysine-HCl (ε-PLH) onto corn starch so as to prepare antimicrobial starch, and prepare films based the grafted starch and characterize the properties of both grafted starch and films to provide reference for application of starch. Coupling agent was utilized to graft starch and ε-PLH and the chemical structure, micromorphology, thermal stability and antimicrobial properties of grafted starch were determined. Films were prepared by the modified starch, polylactic acid (PLA) and poly (butylene adipate co-terephthalate) (PBAT) through melt extrusion process. The mechanical and antimicrobial properties of films were determined. FTIR results showed that ε-PLH was grafted onto starch successfully, and thermogravimetric analysis (TGA) showed decrease in the initial decomposition temperature of grafted starch. The films with 30% grafted starch presented better tensile strength. Moreover, the films with 30% grafted starch showed 46.53% and 68.81% inhibitory rate against E.coli and S.aureus respectively. In conclusion, grafting ε-PLH is an approach that effectively modifies starch and the grafted starch/PBAT/PLA films have great practical potential.