Hierarchical porous structure, which include macropores, minor pores, and micropores in scaffolds, are essential in the multiple biological functions of bone repair and regeneration. In this study, patient-customized calcium-deficient hydroxyapatite (CDHA) scaffolds with three-level hierarchical porous structure were fabricated by indirect 3D printing technology and particulate leaching method. The sacrificial template scaffolds were fabricated using a photo-curing 3D printer, which provided a prerequisite for the integral structure and interconnected macropores of CDHA scaffolds. Additionally, 20 wt% pore former was incorporated into the slurry to enhance the content of smaller pores within the CDHA-2 scaffolds, and then the CDHA-2 scaffolds were sintered to remove the sacrificial template scaffolds and pore former. The obtained CDHA-2 scaffolds exhibited interconnected macropores (300–400 μm), minor pores (∼10–100 μm), and micropores (< 10 μm) distributed throughout the scaffolds, which could promote bone tissue ingrowth, increase surface roughness, and enhance protein adsorption of scaffolds. In vitro studies identified that CDHA-2 scaffolds had nanocrystal grains, high specific surface area, and outstanding protein adsorption capacity, which could provide a microenvironment for cell adhesion, spreading, and proliferation. In addition, the murine intramuscular implantation experiment suggested that CDHA-2 scaffolds exhibited excellent osteoinductivity and were superior to traditional BCP ceramics under conditions without the addition of live cells and exogenous growth factors. The rabbit calvarial defect repair results indicated that CDHA-2 scaffolds could enhance in situ bone regeneration. In conclusion, these findings demonstrated that the hierarchical porous structure of CDHA scaffolds was a pivotal factor in modulating osteoinductivity and bone regeneration, and CDHA-2 scaffolds were potential candidates for bone regeneration.