Studies on soybean protein–polyphenol complexes mainly focus on the effects of non-covalent/covalent interactions on the structure and function of the complexes, and there are few studies on the stability and in vitro digestion mechanism of these complexes. We investigated the effects of non-covalent/covalent binding of catechin with soy protein isolate (SPI) on the structure, aggregation, stability and digestive characteristics of the SPI-Catechin complexes. SPI-Catechin non-covalent/covalent complexes were prepared under neutral (pH 7.0) or alkaline (pH 9.0) conditions, and the protein:polyphenol ratio was optimized. The interaction of SPI and catechin disordered the secondary structure and exposed more hydrophobic residues to a hydrophilic microenvironment. SPI-Catechin covalent complexes exhibited higher thermal stability, storage stability, and antioxidant activity compared to non-covalent complexes. Results of in vitro digestion showed that SPI-Catechin covalent complexes can substantially (up to ∼86%) improve the bioaccessibility of catechin. The stronger anti-digestion ability of the covalent complex might be due to the more complete structure of 7S and 11S subunits in the digestion products. This study provides a theoretical basis for the application of SPI-Catechin non-covalent/covalent complexes as functional components of plant protein drinks. • The degree of binding between catechin and SPI was affected by the ratio and pH value. • SPI-Catechin covalent complexes were more stable than non-covalent complexes. • Non-covalent/covalent binding of SPI improved the bioaccessibility of catechin. • SPI-Catechin covalent complexes had stronger anti-digestive ability.