A hierarchical, intrafibrillarly mineralized collagen (HIMC) is achieved through a selective mineralization progress in the collagenous gap regions mediated by poly(acrylic acid) with appropriate molecular weight. The associated topographical features directly correlate with nanomechanical heterogeneities of the HIMC to accommodate a broad range of external loads. Moreover, this hierarchically staggered nanostructure provides an optimized microenvironment to improve bone regeneration by instructing host cells.