Main failure modes of honeycomb flooring undergoing bending load were studied and an optimization model based on failure factors was set up. According to the optimization design criterion of the flooring structure, the evaluation function based on four objective functions was constructed, which were high flexural rigidity, high strength requirement, high inherent frequency, and low mass of the flooring, with four constraint conditions, which were stability, buckling extreme, shear strength, and stiffness. The optimal value of dimensional parameters was obtained and the parameters of mechanical property were calculated through them. Strength calculation formula was utilized to check the strength of the structure. The computational results showed that the optimized honeycomb container flooring meets the application demand.