In this study, aglycone-type flavonoids (hesperitin and naringenin) and glycoside-type flavonoids (hesperidin and naringin) were encapsulated into pea protein isolate (PPI) nanoparticles by the pH-shifted method. The effect of glycosylation of flavonoids on their encapsulation efficiency in PPI carrier and their interaction with carrier molecules was explored by molecular docking along with other traditional experiments. The results showed that all flavonoids were well encapsulated in PPI nanoparticles, and hydrophobic interactions and hydrogen bonds were the important driving forces contributing to the formation of flavonoids-loaded PPI nanoparticles. However, flavonoid aglycone molecules encapsulated into nanoparticles were more than their glycoside counterparts, and flavonoid aglycones preferred to reduce fluorescence intensity and storage stability of PPI nanoparticles compared with their glycosides. Additionally, flavonoid aglycones formed less hydrogen bonds with protein compared with their corresponding glycosides. Altogether, this study can be meaningful for the selection of flavonoids more suitable for encapsulation into delivery carriers.