The biotoxicity of nanomaterials is very important for the application of nanomaterials in biomedical systems. In this study, proteins with varying secondary structures (α-helices, βsheets, and mixed α/β structures) were employed to investigate the biological properties of three representative two-dimensional (2D) nanomaterials; these nanomaterials consisted of black phosphorus (BP), graphene (GR), and nitrogenized graphene (C 2 N) and were studied using molecular dynamics simulations. The results showed that the α-helix motif underwent a slight structural change on the BP surface and little structural change on the C 2 N surface. In contrast, the structure of the β-sheet motif remained fairly intact on both the BP and C 2 N surfaces. The αhelix and β-sheet motifs were able to freely migrate on the BP surface, but they were anchored to the C 2 N surface. In contrast to BP and C 2 N, GR severely disrupted the structures of the α-helix and β-sheet motifs. BBA protein with mixed α/β structures adsorbed on the BP and C 2 N surfaces and exhibited biological behaviors that were consistent with those of the α-helix and β-sheet motifs. In summary, C 2 N may possess better biocompatibility than BP and GR and is expected to have applications in the biomedical field. This study not only comprehensively evaluated the biological characteristics of nanomaterials but also provided a theoretical strategy to explore and distinguish the surface characteristics of nanomaterials.