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Design of prestressed concrete aqueduct is involved in multidimensional variables non-linear optimal problem, although there are many traditional optimization methods. However, more or less disadvantages of these traditional methods affect optimization results. As a result, a new method of Improved Genetic Algorithm which have better search capability and global optimization is applied in Xinjiang Nilka prestressed concrete aqueduct design. The result shows that the improved algorithm is feasible and effective, which provides references to similar projects design in the future.