In the process of crop cultivation, the application of a fertilizer solution with appropriate pH value is more conducive to the absorption of nutrients by crops. If the pH of the irrigation water and fertilizer solution is too high, it will not only be detrimental to the absorption of nutrients by the crop, but will also damage the structure of the soil. Therefore, the precise regulation of pH in water and fertilizer solutions is very important for agricultural production and saving water and fertilizer. Firstly, the article investigates the hybrid control of fertilizer and water conditioning systems, then builds a fuzzy preprocessing controller and a neural network proportional–integral–differential controller, and optimizes the neural network parameters by means of an improved particle swarm algorithm. The effectiveness of the controller was verified by comparison with the common proportional–integral–differential control and fuzzy algorithm control for fertilizer control and fuzzy preprocessing neural network control. Simulation experiments for this study were designed through the MATLAB/Simulink simulation platform, and the simulation results show that the algorithm has good tracking and regulation capabilities in the system. Finally, the four control algorithms are experimentally validated under different pH regulations using designed field experiments. The results show that, compared with other control algorithms, the control algorithm in this paper has a smaller overshoot and good stability with a shorter rise time, which can achieve the purpose of better regulating the fertilizer application system.