In order to explore the effects of thymol on the antimicrobial activity, structure, physical properties and fresh-keeping application of starch/PBAT composite films, different contents of thymol (0, 1%, 3% and 5%) were used to prepare antimicrobial composite films by extrusion blow molding. The results indicated that tourier transform infrared spectroscopy showed there was intermolecular hydrogen bonding force among starch/PBAT and thymol. The inhibition effect on Botrytis cinerea and the preservation effect of cherry tomato of the composite film were significantly improved, the hardness and nutritional characteristics of cherry tomato were maintained, and the fruit decay rate was reduced. The addition of thymol increased the water vapor permeability of the starch based composite films, but reduced the interaction between the composite film and water. Although thymol reduced the mechanical properties of the composite film, high concentration of thymol further improved the mechanical properties. In conclusion, the high concentration of thymol improved the comprehensive properties of starch composite film, and proved the application prospect of the film as active food packaging material.