During the variable rate irrigation operation of large-sized lateral moving irrigation system based on pulse width modulation (PWM) technique, it is quite difficult to solve the flow rate of each sprinkler from the designed prescriptions of management zones because the spraying areas of sprinklers will overlap with each other. At the beginning, the overlapped water distribution in lateral direction, and the two-dimensional contour plot of overlapped water distribution were gotten based on the feature of single sprinkler water distribution of Nelson R3000. Then four sprinklers were determined to control a management zone and the water distribution rate of spraying area was solved. And on this basis a weighted average method and a genetic algorithm (GA) method based on genetic algorithm were proposed to perform sprinkler flow rate distribution according to the prescription. It was found that the solution accuracy can reach 5% when the change between adjacent prescriptions was less than 33% of the maximum prescription by analyzing the irrigation error in management zone. In order to make up for the reduction of irrigation uniformity caused by GA method, a combined method of weighted average method and GA method was put forward. Related examples had showed that the irrigation error caused by the saltation of adjacent prescriptions can be reduced by the combined method effectively and the irrigation uniformity of management zones where prescriptions changed little can also be guaranteed at the same time. By changing the mapping relationship between sprinkler flow rate and actual irrigation volume in each management zone, this method can be extended to more than four sprinklers controlling a management zone.