Se-enriched peptides serve various physiological functions and are crucial sources of Se. This study found the Se content of yellowfin tuna dark meat was 18.34 mg/kg (dry weight), making it an ideal natural source of Se-enriched peptides. We used five different enzymatic treatments to prepare Se-enriched protein hydrolysates from dark meat. Among them, the trypsin-generated protein hydrolysate showed the highest α-glucosidase inhibition activity. It was then fractionated by ultrafiltration followed by RP-HPLC, and the sequences of Se-enriched peptide obtained were identified from the most active fraction by LC-MS/MS. Subsequently, KPLSeCPK was screened by in silico analyses and validated by the α-glucosidase activity inhibition experiment (IC50=0.828 mM). Molecular docking and inhibition kinetics assay further demonstrated the interaction between KPLSeCPK and α-glucosidase, suggesting its potential as a novel hyperglycemic inhibitor. Moreover, KPLSeCPK lessened IR and boosted antioxidant capability of IR-HepG2 cells. Thus, KPLSeCPK provides a valuable reference for efficiently utilizing natural organic Se.