In order to solve the lack of optimization and comparison of the previous schemes in the irrigation and water conservancy project reconstruction, the engineering design and planning are difficult to reach the best state, resulting in water resource waste and other problems. In this paper, genetic algorithm optimization technology of the irrigation canal system is studied, in-depth learning technology of image processing is elaborated, the rectangular optimization model is established, and the optimal nonlinear design of trapezoidal and U-shaped sections of irrigation channel is verified by engineering examples. According to the geographical location, water source, irrigation area, irrigation area, and designer’s experience, two possible irrigation scheme layouts have been determined, and the trapezoidal section has been optimized. The results show that the value of the objective function decreases rapidly with the increase of iteration time. Scheme 1 has stabilized for about 19 generations. Scheme 2 tends to be stable for about 25 generations. The optimization results of the U-shaped section show that scheme 1 is stable for about 43 generations, while scheme 2 tends to be stable for about 60 generations. By comparing the optimal schemes of the trapezoidal section and the U-section, it can be found that the water supply cost of the U-section is low. Therefore, under the condition of layout scheme 2, the U-shaped section is the best scheme. The calculation shows that under the same conditions, the trapezoidal section area is about 45% larger than the U-shaped section area. Although the trapezoidal section is adopted in the original project, the U-shaped section is recommended when construction conditions permit. The optimization method can quickly determine the overall optimization scheme of irrigation channels. The water supply cost depends on the final optimized objective function value, which is used as the reference basis for formulating the water supply price. The optimal design scheme should not only meet the provisions of engineering practice but also meet the requirements of the lowest water supply cost.