Mineralized collagen fibrils are important basic building blocks of calcified tissues, such as bone and dentin. Polydopamine (PDA) can introduce functional groups, i.e., hydroxyl and amine groups, on the surfaces of type I collagen (Col-I) as possible nucleation sites of calcium phosphate (CaP) crystallization. Molecular bindings in between PDA and Col-I fibrils (Col-PDA) have been found to significantly reduce the interfacial energy. The wetting effect, mainly hydrophilicity due to the functional groups, escalates the degree of mineralization. The assembly of Col-I molecules into fibrils was initiated at the designated number of collagenous molecules and PDA. In contrast to the infiltration of amorphous calcium phosphate (ACP) precursors into the Col-I matrix by polyaspartic acid (pAsp), this collagen assembly process allows nucleation and ACP to exist in advance by PDA in the intrafibrillar matrix. PDA bound to specific sites, i.e., gap and overlap zones, by the regular arrangement of Col-I fibrils enhanced ACP nucleation and thus mineralization. As a result, the c-axis-oriented platelets of crystalline hydroxyapatite in the Col-I fibril matrix were observed in the enhanced mineralization through PDA functionalization.