Rice bran protein (RBP) aggregates were prepared by heating of RBP solution at 90 °C for 4 h at pH 2, 7, or 11 and used for preparing of packaging films. The structure and properties of RBP aggregates and RBP-based films were characterized with sodium dodecyl sulfate–polyacrylamide gel electrophoresis, transmission electron microscopy, scanning electron microscope, differential scanning calorimetry, Fourier transform infrared spectroscopy and circular dichroism. The results showed formation of fibrillar, globular, and large molecular protein aggregates during the heating at pH 2, 7 and 11. The heat-aggregated RBP-based films exhibited lower opacity, moisture content, water solubility, and water vapor permeability than those of untreated RBP-based films. Also, improved mechanical and thermal properties were found for the heat-aggregated RBP-based films. In addition, the heat-aggregated RBP-based film at pH 11 showed homogenous and smooth surface as well as compact appearance compared with the untreated RBP-based films or heat-aggregated RBP-based film at pH 2 or 7. Furthermore, the secondary structure of heat-aggregated RBP film exhibited an increase in β-sheet content and molecular interactions through non-covalent bonds. The obtained results indicated that formation of protein aggregates could improve physical, mechanical, and thermal properties of RBP-based film, especially at pH 11.