Abstract: The changes in functionality (solubility, emulsification, gelation) and digestibility of quercetin-soy protein isolate and rutin-soy protein isolate complexes were analyzed in this paper. The interaction was studied by UV-Vis spectroscopy and fluorescence spectroscopy. The mechanism, the type of fluorescence quenching, the number of binding sites and thermodynamic parameters were analyzed. The results showed that quercetin and rutin could improve the functional properties of SPI. When the addition of quercetin and rutin were 8%, the hardness of SPI gel could be increased by 23.23% and 187.18%, respectively. The EAI, ESI and solubility of SPI increased first and then tended to level off. When the addition amount was 6% and 4%, the emulsifying activity and solubility reached the highest respectively, which were increased by 20.84% and 10.06% compared with SPI. With the increase of rutin addition, the EAI, ESI and solubility of SPI first increased and then decreased slightly. When the addition amount was 4% and 6%, the emulsifying activity and solubility reached the highest respectively, which was 26.17% and 19.27% than that of SPI. In addition, the interaction of quercetin and rutin with SPI could also improve the bioavailability of the protein. Further research on the interaction mechanism between the two flavonoid polyphenols and SPI showed that the fluorescence spectra of the two interacting complexes were blue-shifted, quercetin, rutin and SPI spontaneously combine, and mainly acted through hydrogen bonding and van der Waals forces. The interaction mechanism of quercetin, rutin and SPI was dynamic quenching and static quenching, respectively.