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Soybean protein isolate (SPI) exhibits remarkable sensitivity to environmental changes, particularly alterations in pH value during the neutralization process. Even minor fluctuations can have a profound impact on the structure and functional properties of the protein. Revolving around the addition of NaOH to regulate the pH value of the curd, and analysis of SPI’s structure and functional attributes was done by using infrared and endogenous fluorescence spectra. It was revealed that SPI displayed excellent foaming properties under neutral conditions, while its emulsification capabilities excelled under slightly more alkaline conditions. Specifically, pH value of 7 yielded the best foaming type, while pH value of 8.5 led to superior foaming properties alongside optimal emulsification. In order to fine-tune the neutralization of a 25L soybean SPI section, a pH value control system was established, and the entire production process was simulated by using Matlab. Dynamic linear and static nonlinear fitting techniques were employed, with a combination of fuzzy adaptive control and the Wiener model utilized to regulate the amount of alkali added to the neutralization tank. The adjustment time of 37.4s achieved when the pH value in the neutralization tank was set to 7. Likewise, at pH value of 8.5, the adjustment time remained efficient at 33.4s, while the SPI emulsion activity index reached 69.35m2/g. Notably, the system successfully avoided any overshooting of alkali during the process, ensuring precise control and stability throughout. To summarize, the research emphasized the significance of pH value control during the neutralization of soybean protein isolate. The findings can provide important insights into optimizing SPI’s structure and functional properties, which can have significant implications for its applications in the food and industrial sectors.