When the irrigation area uses surface water as its water source and has sufficient supply, the optimization of the micro-irrigation pipe network requires determining the reasonable control area and layout form of individual micro-irrigation systems and conducting optimized design. The current pipe network optimization method is not applicable to the optimization of random water supply micro-irrigation pipe network systems under this situation. In order to achieve the synchronization optimization of layout and pipe diameter for random water supply micro-irrigation pipe network systems without limiting the area, and propose the optimal design criteria, a mathematical model for optimizing micro-irrigation main pipe network was established, and a model solution method based on a hybrid encoding genetic algorithm was provided. The correlation between the annual cost per unit area of the main pipe network and its layout was analyzed and the influence of lateral diameter, emitter design discharge, emitter spacing, and emitter emission exponent on the unit area annual cost of main pipe network and micro-irrigation pipe network system was analyzed. The results of example calculations showed that the unit area annual cost of the micro-irrigation pipe network system optimized based on the model with maximum control area for lateral double-sided layout was the lowest, while the unit area annual cost of the micro-irrigation pipe network system optimized based on the model with minimum unit area annual cost for lateral one-sided layout was the highest. Compared with the model with the minimum unit area annual cost for lateral one- sided layout, the percentage reduction in unit area annual cost of the micro-irrigation pipe network system optimized based on the model with maximum control area for lateral double-sided layout was 4.46% to 15.74% . In actual engineering projects, using smaller lateral diameters, emitter design discharges, emitter emission exponents, larger spacing between emitters, optimizing subunit based on the model with maximum control area for lateral double-sided layout, can effectively reduce costs. The results can provide a basis for the optimization design of random water supply micro-irrigation pipe network systems without limiting the area.