Xinjiang is the largest cotton-producing region in China, but it faces a severe shortage of water resources. According to relevant studies, the cotton yield does not significantly decrease under appropriate limited water conditions. Therefore, this paper proposes a water and fertilizer integrated control system to achieve water and fertilizer conservation in the process of cotton field cultivation. This paper designs a fuzzy neural network Proportional–Integral–Derivative controller based on the improved Wild Horse Optimizer to address the water and fertilizer integrated control system’s time-varying, lag, and non-linear characteristics. The controller precisely controls fertilizer electrical conductivity (EC) by optimizing parameters through an improved Wild Horse Optimizer for the initial weights from the normalization layer to the output layer, the initial center values of membership functions, and the initial base width of membership functions in the fuzzy neural network. The performance of the controller is validated through MATLAB simulation and experimental tests. The results indicate that, compared with conventional PID controllers and fuzzy PID controllers, this controller exhibits excellent control accuracy and robustness, effectively achieving precise fertilization.