The development of biocompatible nanomaterials for smart drug delivery and bioimaging has attracted great interest in recent years in biomedical fields. Here, the interaction between the recently reported nitrogenated graphene (C2N) and a prototypical protein (villin headpiece HP35) utilizing atomistic molecular dynamics simulations is studied. The simulations reveal that HP35 can form a stable binding with the C2N monolayer. Although the C2N–HP35 attractive interactions are constantly preserved, the binding strength between C2N and the protein is mild and does not cause significant distortion in the protein's structural integrity. This intrinsic biofriendly property of native C2N is distinct from several widely studied nanomaterials, such as graphene, carbon nanotubes, and MoS2, which can induce severe protein denaturation. Interestingly, once the protein is adsorbed onto C2N surface, its transverse migration is highly restricted at the binding sites. This restriction is orchestrated by C2N's periodic porous structure with negatively charged “holes,” where the basic residues—such as lysine—can form stable interactions, thus functioning as “anchor points” in confining the protein displacement. It is suggested that the mild, immobilized protein attraction and biofriendly aspects of C2N would make it a prospective candidate in bio- and medical-related applications.