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The problem of selecting the best pattern of layout and pipe diameter of each pipe in the micro-irrigation pipe network system has long been given considerable attention by engineers and obtained numerous research results. Micro-irrigation pipe network system is composed of rotational irrigation network (manifold and lateral) and continuous irrigation network (main and submain pipe). Previous studies did not treat micro-irrigation pipe network system as an integral and can not realize the simultaneous optimization of layout and pipe diameter combination. In addition, research results can not be applied to the optimization of pumping microirrigation pipe network system for large irrigation area. The optimization method of pumping micro-irrigation pipe network system was proposed. The mathematical models of rotational irrigation network and continuous irrigation network were established. The best control area, layout and pipe diameter of rotational and continuous irrigation network can be obtained simultaneously by solving the mathematical model with dual coding genetic algorithm. Commercial pipe diameters can be obtained through the optimization without adjustment. Examples showed that the algorithm was of good convergence and high precision on optimization problem of pumping microirrigation pipe network system. Compared with the traditional design scheme, the annual total cost per unit irrigated area of optimized design scheme for rotational irrigation network was reduced by 14.85%~35.59%, and the annual total cost per unit irrigated area of optimized design scheme for continuous irrigation network was reduced by 4.12%~12.99%. The simultaneous optimization method of layout and pipe diameter can be applied to the optimal design of pumping microirrigation pipe network system on uniformly sloping fields which with sufficient water source. The research result had important theoretical value and practical significance in the optimization of pumping micro-irrigation pipe network system for large irrigation area.