The dense structure of soy protein isolate (SPI) usually leads to reduced stability and digestibility, limiting its practical application. Protease hydrolysis and polyphenol complexation are considered green means to modify the protein to improve its properties. The study aimed to address the persistent challenges associated with the stability and digestibility of SPI through dual modification of enzymatic hydrolysis and polyphenol. Complexes of varying concentrations of phlorotannins (0, 0.2, 0.5, 1.0, 2.0 mg/mL) with SPI and SPI hydrolysate (SPIH) were prepared through both covalent and noncovalent interactions, and the complex structure, stability, and digestive properties were further investigated. Raman spectroscopy, UV spectroscopy, 3D fluorescence spectroscopy, free sulfhydryl groups, and SEM were employed, and the results showed a synergistic transformation in the SPI structure upon enzymatic hydrolysis and PT addition, which was manifested by the exposure of aromatic amino acids, the formation of intermolecular disulfide bonds, the decrease in surface free sulfhydryl groups (1.04 mu mol/ g) and an increased in microscopic network structure. The SPIH-PT covalent complexes (CHP) displayed excellent stability in pH, ionic, thermal (73.79 degrees C), storage (0.55) and freeze-thaw outperforming non-covalent complexes. In vitro gastrointestinal simulated digestion reduced the complexes particle size. The particle size of the digested product increased with increasing PT concentration (increased to 359.70 nm). FTIR of the digested products revealed gradual increase in beta-turn and beta-sheet content to 34.50% and 19.80%. Enzymatic hydrolysis and polyphenol covalent complexation effectively enhanced the antidigestive properties of the complexes (as low as 19.03%), increased the free amino acid content, improved the antioxidant capacity, and elevated the polyphenol bioaccessibility (up to 88.87%). This work will offer theoretical references to research on the stability and digestion mechanisms of protein hydrolysate-PT complexes, and provide data support for its application in functional foods.