This study aimed to develop an antimicrobial food preservation material based on kaolin (KL) encapsulated with thyme essential oil (TEO). The release of TEO in the TEO/KL composite was controlled by the relative humidity inside of food packaging. The morphology and element distribution of TEO/KL composites were determined with scanning electron microscopy and energy dispersive spectrometer. The release profiles illustrated that the release of TEO accelerated with the increase of relative humidity (30%, 60% and 90%) due to the high porosity and hydrophilicity of KL. The antimicrobial results illustrated that the activity of Escherichia coli (E. coli), Staphylococcus aureus (S. aureus) and Botrytis cinerea (B. cinerea) remarkably reduced after treating with the TEO/KL composite (1.0, 1.5 and 2.0 mg), and the inhibition rate reached over 99%. The cytotoxicity assays demonstrated good biocompatibility and biosafety of TEO/KL applied to food preservation. This composite also exhibited a desirable preservation effect on strawberries and grapes and displayed great potential in food industry.