In order to screen bioactive peptides against SARS-CoV-2 from food raw materials, Mizuhopecten yessoensis myosin was selected as the target sequence, which was enzymatically digested in silico, and then the toxicity and bioactivity of the peptides were predicted. The non-toxicity peptides with activity scores exceeding 0.5 were selected, and SARS-CoV-S/ACE2 complex protein and COVID-19 Mpro hydrolase were selected as targets for molecular docking to identify their viral resistance. The molecular docking results showed that the peptide CSNAIPEL could bind to the two key amino acids GLN42 and GLU329 on the SARS-CoV-S/ACE2 complex protein, and the LibDock Score was 136.03. LPIY could not only combine with ASP38 and TYR491 on the SARS-CoV-S/ACE2 complex protein, but also potentially combine with THR24, THR25 and THR26 on COVID-19 Mpro, and the LibDock Score was 142.85 and 168.04 respectively. QRPR combined with THR24, THR25 and THR26 on the COVID-19 Mpro hydrolase crystal, and the LibDock Score was 154.93. In summary, peptides CSNAIPEL, LPIY and QRPR exhibited well anti-SARS-CoV-2 capability. This study could provide novel ideas for the development of new function foods of anti-SARS-CoV-2 in the future.