The interaction and action mechanism of starch with different phenolic compounds were investigated. By using scanning electron microscope, nuclear magnetic resonance, Fourier transform infra-red spectroscopy and thermogravimetric analysis, phenolic compounds exhibited the significant effects on the morphology, intensity of hydrogen bond, crystalline structure and thermal stability of starch, respectively. Furthermore, according to the analysis of molecular dynamics simulation by using short-chain glucose (SGS) as model, phenolic compounds could change the spatial configuration of starch, and had the obvious effects on the formation of hydrogen bonds (including intra- and intermolecular hydrogen bonds) and the strength of binding free energy. Meanwhile, epigallocatechin gallate possessed the strongest capacity to change the spatial configuration of starch with the consistent hydrogen bond occupancy and the lowest binding free energy. All present results suggested that phenolic compounds might be potentially utilised for improving the quality of starch in food industry.