Corn flours industry consumes large amounts of energy (98 kWh/ton) in the processing of corn to corn flours. The main source of energy have been fossil fuel which availability is declining overtime. A continued dependency on this energy source would become constraining factor in the very near future. In addition, the production of corn flours produced wastes that can be used as a source of alternative sustainable energy. The purpose of this research was to develop a model of the mass balance and energy of corn flours processing industry as an energy independent system so as to minimize dependence on fossil energy. The results are expected to be a reference to the development of independent or more efficient energy corn flours industry. The model was developed to depict the actual situation of corn flours production process. The output of the model showed that obtained yield of corn flours is 31%. The wastes are cobs and corn husk that can be utilized to generate energy as much as 3,870 kWh from combustion technique with boiler at 68% efficiency. Therefore, corn flours industry can be energy independent.