The walnut meal is rich in nutrients such as protein from the kernel and polyphenolic compounds from the seed coat. However, the influences of seed coat polyphenols on walnut protein (WP) hydrolysis remained unclear. In this study, our findings indicated that polyphenols induced alterations in the secondary structure and amino acid composition of WP. These changes resulted in both a hindrance of hydrolysis and an enhancement of acetylcholinesterase (AChE) inhibition. Furthermore, four peptides of 119 identified peptides (LR, SF, FQ, and FR) were synthesized based on higher predicted bioactivity and Vinascores in silico. Among them, FQ showed interaction with amino acid residues in AChE through the formation of four π-π stacking bonds and two hydrogen bonds, resulting in the highest AChE inhibitory capacity. The combination index showed that chlorogenic acid derived from the seed coat and FQ at the molar ratio of 1:4 exhibited synergistic effects of AChE inhibition.