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Calcium phosphate bio-ceramics are osteo-conductive, but it remains a challenge to promote the induction of bone augmentation and capillary formation. The surface micro/nano-topography of materials can be recognized by cells and then the cell fate are mediated. Traditional regulation methods of carving surface structures on bio-ceramics employ mineral reagents and organic additives, which might introduce impurity phases and affect the biological results. In a previous study, a facile and novel method was utilized with ultrapure water as the unique reagent for hydrothermal treatment, and a uniform hydroxyapatite (HAp) surface layer was constructed on composite ceramics (β-TCP/CaSiO3) in situ. Further combined with 3D printing technology, biomimetic hierarchical structure scaffolds were fabricated with interconnected porous composite ceramic scaffolds as the architecture and micro/nano-rod hybrid HAp as the surface layer. The obtained HAp surface layer favoured cell adhesion, alleviated the cytotoxicity of precursor scaffolds, and upregulated the cellular differentiation of mBMSCs and gene expression of HUVECs in vitro. In vivo studies showed that capillary formation, bone augmentation and new bone matrix formation were upregulated after the HAp surface layer was obtained, and the results confirmed that the fabricated biomimetic hierarchical structure scaffold could be an effective candidate for bone regeneration.