Conventionally, when optimizing a structure, the single target structural optimization design method is usually used. However, this design result often can not meet with the multiple requirements of construction; furthermore its optimizing efficiency is low; so its application is limited. And more, as the objective function being generally continuous variable, the optimized result is not the structural module and this is inconvenient for construction. This paper, taking the structural strain energy and the cost of construction as the targets to be optimized, and the design variable being discrete, provides multiple-target earthquake-resistant optimization design method aiming at obtaining the largest stain energy and the lowest construction cost, and established the function relation formula between the strain energy and the cost of construction and obtained the satisfied result. The highlight of this process is adopting discrete variables as the design variables, therefore the optimized results (cross-sectional dimensions) will conform to the requirements of structural module and the engineering practice. The optimization process presented in this paper conforms entirely to the national standards: “Code for Design of Reinforced Concrete Structures” (GB50010-2002) and “Code for Earthquake-resistant Design of Buildings” (GB50011). The theory and methods presented in this paper will be helpful for the structural design engineers and the researchers.