Unraveling the interaction mechanisms of type I collagen with various inorganic nanoparticles is of pivotal importance to construct collagen-based bionanocomposites with hierarchical structures for biomedical, pharmaceutical, and other industrial applications. In this study, synthetic two-dimensional Laponite nanoplatelets (LAP NPs) are surface-functionalized with tetrakis(hydroxymethyl) phosphonium sulfate (THPS) for reinforcing their incorporation with type I collagen matrix by focusing on the influences of the interactions on the hierarchical structures of the collagen. Our results indicate that the LAP NPs can be successfully surface-functionalized with THPS via covalent bonds between the amine-functionalized NPs and the hydroxymethyl groups of THPS. Moreover, the resulting NPs can be well dispersed into the collagen matrix and evenly bound onto the collagen fiber strands and between the collagen fibrils, preserving the native D-periodic banding patterns of the collagen fibrils. The formation of covalent and hydrogen bonds between the collagen and the functionalized NPs can stabilize the intrinsic triple-helical conformation of the collagen, conferring the resulting collagen-based nanocomposites with improved thermal stability and enhanced mechanical properties. We anticipate that a fundamental understanding of the interactions between the collagen and functionalized inorganic nanoparticles would contribute to the design, fabrication, and further application of hierarchical collagen-based bionanocomposites with multifunctions.