Mineralized　collagen　is　a　natural　organic-inorganic　composite.　The　combination　of　organic　collagen　and　inorganic　apatite　to　form　different　nanostructures　is　the　key　to　producing　bone　substitutes　with　biomechanical　properties　that　are　as　identical　to　normal　bone　as　possible.　However,　the　formation　of　apatite　with　different　nanostructures　during　collagen　mineralization　is　unexplored.　Here,　pyrophosphate　(Pyro-P),　as　an　important　hydrolysate　of　adenosine　triphosphate　in　the　body,　was　introduced　to　prepare　mineralized　collagen　under　the　regulation　of　alkaline　phosphatase　(ALP)　and　orthophosphate　(Ortho-P).　Scanning　electron　microscopy　(SEM)　and　transmission　electron　microscopy　(TEM)　results　showed　that　mineralized　collagen,　which　combined　with　different　crystallinities　and　multilayered　structured　apatite,　was　successfully　prepared.　A　combination　of　ion　chromatography　(IC),　Fourier　transform　infrared　(FTIR)　spectroscopy,　circular　dichroism　(CD),　and　thermogravimetry　(TG)　analyses　revealed　the　crucial　role　of　Ortho-P　in　the　formation　of　multilayered　flower-shaped　apatite　with　different　crystallinities　and　in　the　maintenance　of　mineralization　balance.　Mineralization　balance　is　of　great　significance　for　maintaining　normal　bone　morphology　during　bone　regeneration.　Overall,　our　results　provide　a　promising　method　to　produce　new　bone　substitute　materials　for　the　repair　of　large　bone　defects　and　a　deeper　insight　into　the　mechanisms　of　biomineralization.