Perilla seed meal is an important agricultural by-product of perilla oil extraction. The antioxidant and anti-aging activities of perilla seed meal protein hydrolysate were investigated, and the bioactive peptides were identified to maximize the utilization of perilla seed meal resources. Anti-aging peptides were identified using a combination of peptidomics and in silico bioinformatics. Furthermore, the potential molecular mechanism of these peptides was explored through molecular docking and RT-PCR. The results showed a significant anti-aging properties of F2 (MW 3 kDa ∼5 kDa) by inhibition of reactive oxygen species (ROS) production and β-galactosidase activity. Nine novel peptides were identified from F2 and subsequently synthesized to explore their bioactivities. The two peptides, NFF and PMR, were found to promote the proliferation of keratinocytes (HaCaT cells) and suppress the level of ROS and the activity of β-galactosidase. Both peptides exhibited a strong binding affinity with the Keap1 protein. Additionally, NFF and PMR downregulated the expression of matrix metalloproteinases (MMPs) and the degradation of collagens (COLs). The potential molecular mechanism underlying the anti-aging properties of perilla seed meal peptides might involve the competitive binding of Keap1 to facilitate the release of Nrf2 and activation of NF-κB signal pathway. This study provides a theoretical basis for the application of perilla seed meal peptides in functional cosmetics and presents a novel perspective for the investigation of additional food-derived peptides.