The traditional method applying to solve continuous variable optimization problems is not suit for flume structural optimization design with hybrid discrete variable. According to the mathematical model of structural optimum design of the prestressed U-shell flumes, differential evolution (DE) algorithm was introduced to flume structural optimization design. In order to improve the population’s diversity and the ability of escaping from the local optimum, a self-adapting crossover probability factor was presented. Furthermore, a chaotic sequence based on logistic map was employed to self-adaptively adjust mutation factor based on linear crossover, which can improve the convergence of DE algorithm. Dynamic penalty function, to transform the constrained problem to unconstrained one, was employed. The result shows that, compared with the original design scheme, the optimization design scheme can greatly reduce the amount of prestressed reinforcement. The construction cost of both the flume and the whole project can be reduced accordingly.