The occurrence of fractures has emerged as one of the most prevalent injuries in the human body. In bone reconstruction surgery, after the implantation of porous hydroxyapatite materials, there is an initial infiltration of body fluids into the porous implant, followed by biomineralization-mediated apatite crystal formation and the subsequent ingrowth of bone cells. Despite extensive research efforts in this field, previous investigations have primarily focused on the formation of apatite crystals on exposed surfaces, with limited literature available regarding the formation of apatite crystals within the internal microstructures of bone implants. Herein, we demonstrate the occurrence of dynamic biomineralization within a three-dimensional porous hydroxyapatite/wollastonite (HA/WS) skeleton, leading to the abundant formation of nano-sized apatite crystals across diverse internal environments. Our findings reveal that these apatite nanocrystals demonstrate distinct rates of nucleation, packing densities, and crystal forms in comparison to those formed on the surface. Therefore, the objective of this study was to elucidate the temporal evolution of biomineralization processes by investigating the microstructures of nanocrystals on the internal surfaces of HA/WS three-dimensional porous materials at distinct stages of biomineralization and subsequently explore the biological activity exhibited by HA/WS when combined with cell investigation into apatite crystal biomineralization mechanisms at the nanoscale, aiming to comprehend natural bone formation processes and develop efficacious biomimetic implants for tissue engineering applications. The simultaneous examination of bone cell attachment and its interaction with ongoing internal nanocrystal formation will provide valuable insights for designing optimal scaffolds conducive to bone cell growth, which is imperative in tissue engineering endeavors.