In this study, quercetin (Que) was encapsulated for controlled release during gastrointestinal digestion using zein-soy isolate protein (SPI) composite nanoparticles that were made following an antisolvent precipitation technique. The average particle size of the composite nanoparticles ranged from 182.1 to 230.9 nm, and the polydispersity index (PDI) was small (0.105-0.323). The microstructure revealed that the composite nanoparticles were spherically distributed and that Que. was embedded on the surface of the nanoparticles. Que. has an encapsulation efficiency of up to 93.3 %. Spectrum analysis, molecular docking and zeta potential measurements revealed that the interactions between the composite nanoparticles and Que. occurred mainly through hydrophobic interactions, hydrogen bonding, and electrostatic interactions. Compared with single zein nanoparticles, the composite nanoparticles showed a significant and controlled release of Que. during the whole simulated gastrointestinal digestion process. This study provides a novel method for the development of a controlled-release drug delivery system for controlling the release of Que.