The purpose of this study was to determine the neuroprotective effect and mechanism of walnut protein hydrolysates (WPH) against memory deficits induced by scopolamine in mice and further to validate the potent neuroprotective peptides identified by integrated approaches of in silico analysis and peptidomics in scopolamine-induced zebrafish. Results showed that a remarkable amelioration on behavioral performance was observed for oral administration of WPH, and disorders of cholinergic system and oxidative stress were normalized in the brains of mice also. Unfortunately, no obvious inflammatory response and anti-inflammatory effect were observed. Additionally, WPH significantly upregulated the expressions of antioxidant defense-related protein (Nrf2) and neurotrophic-related protein (BDNF and CREB). Furthermore, 20 peptides with relatively higher abundance and PeptideRanker scores were predicted by docking to AchE and Keap1. Among them, FY and SGFDAE with the highest binding affinities, -9.8 and -8.0 kcal/mol, were considered as the promising AchE and Keap1 inhibitors, respectively. They were further validated to have neuroprotective capacity in scopolamine-induced zebrafish, indicating that peptidomics and in silico prediction might be the effective approaches to screen neuroprotective peptides.