In the large-scale industrialized production of soymilk, the accurate monitoring of protein content and its secondary structure is crucial to guarantee product quality and enhance nutritional value, while traditional protein detection methods have significant limitations. In this study, Raman spectroscopy was used to characterize the changes in the relative content of protein secondary structures during boiling, in which the α-helix structure was converted to other unstable secondary structures, indicating that the protein was thermally denatured. The study also accurately predicted the soluble protein content of soymilk for the first time by combining Raman spectroscopy and chemometrics based on algorithms such as Partial Least Squares (PLS), Least Squares Support Vector Machines (LSSVM), and Artificial Neural Networks (ANN). The results showed that the relative percentage deviation (RPD) values of all models were greater than 2, indicating that the models all possessed a certain degree of robustness; The PLS-based regression prediction model (with an average RPD value of 3.5592 and an average R2p of 0.9597) had the best overall prediction. The study's results can guide the soymilk production industry into online monitoring of soymilk quality.