An edible hydroxypropyl starch (HPS) based bilayer film with a waterproof layer of zein was successfully prepared through a two-step solvent casting method. The morphology, mechanical properties, as well as water barrier properties of the bilayer film were systematically studied. Results showed that bilayer film presented smooth surface morphology with an improved visibility, and there was an adhesion interface between two layers. Water resistance and UV barrier property, as well as mechanical property, were significantly improved. In addition, the interactions between starch and zein through hydrogen bonding were analyzed by Fourier-transform infrared spectroscopy (FTIR) and molecular dynamics (MD) simulation. In MD simulation, the relative trajectories were dynamically presented. Conjunction of starch and zein through hydrogen bonding among the hydroxyl and amino (carboxyl) groups was identified, and stronger affinity with starch mainly rooted from asparagine (ASN) and tyrosine (TYR) residues.