The specific properties of carbon nanoparticles (NPs) have attracted great attention in applications in biotechnology and biomedicine, e.g., in the field of amyloidosis. To date, it is still indefinable whether carbon NPs would promote or inhibit the fibril formation of amyloid proteins. Here, to uncover the effects of carbon nanoparticles (NPs) including graphene and carbon nanotubes on the aggregation of prion proteins, whose misfolding and aggregation will lead to prion diseases, a ThT fluorescence assay and a molecular dynamics (MD) simulation were performed. The ThT fluorescence assay reveals that both graphene and carbon nanotubes can inhibit the fibril formation of prion proteins, especially graphene. Further MD simulation of the PrP127-147 tetramer with or without carbon NPs suggests that the interactions between prion proteins and carbon NPs reduce the aggregation tendency of PrP127-147 by decreasing the interpeptide interactions and thus inhibiting β-sheet formation. Meanwhile, aromatic residues greatly contribute to the inhibition effects of carbon NPs by a π-π stacking interaction. The obtained results can increase our understanding on the interaction between nanoparticles and amyloid-related proteins.