The effects of six polyphenol copigments on color stability of three monomeric anthocyanins was investigated during wine aging (90 days) through the analysis of chromaticity, thermodynamics and molecular dynamics simulation. Quercetin-3-O-glucoside and caffeic acid exhibited a more pronounced copigmentation effect, with the copigmentation effects of all polyphenol copigments on malvidin-3-O-glucoside and malvidin-3-O-acetylglucoside being significantly greater than that on delphinidin-3-glucoside. The thermodynamic parameters also showed that both the structures of anthocyanins and copigments could influence copigmentation effects, and the quercetin obtained the strongest copigment with malvidin-3-O-glucoside (K = 1572.01). Hydrogen bonds and van der Waals forces facilitated the interaction between anthocyanins and flavonol. The hydroxylated groups of delphinidin-3-glucoside might alter the spatial conformation of the complex, resulting in steric effect. The findings of this study could contribute to a deeper understanding of how copigments and anthocyanin structures influence color stability during wine storage.