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Biofouling caused by protein adsorption and microbial colonization remains a great challenge in many applications. In this work, we synthesized a new type of zwitterionic polypeptoid containing carboxybetaine (CB) moieties (PeptoidCB) through thiol–ene chemistry of poly(N-allylglycine) (PNAG). The zwitterionic antifouling hydrogel was subsequently prepared by co-mixing PeptoidCB with agarose, which exhibited excellent resistance to non-specific protein adsorption and bacterial adhesion. Further, PeptoidCB-modified block copolypeptoids with amphiphilic structure were synthesized to form nanoparticles in an aqueous solution with neglected protein adsorption. The ability of PeptoidCB to resist non-specific protein adsorption and bacterial adhesion makes it a promising candidate for biomedical and industrial applications.