The simple genetic algorithm (SGA) is taken as the global search method, and the traditional direct search method for mixed-discrete variables as the local search method. The improved (hybrid) genetic algorithm (IGA) is obtained by improving the SGA. And through the introduction of penalty constraints, the problem dealing with the constraints in GA is successfully resolved. A mathematical model for structural optimization of aqueduct is established, and computer software is developed for structural optimization of large-scale aqueduct based on IGA. Using this program, the Shuangji River aqueduct is optimized and Rectangle-sectioned aqueduct design plan is obtained. Compared with the original design plan, optimal design is very economical and was adopted by Design Institute.