Adequate new bone regeneration in bone defects has always been a challenge as it requires excellent and efficient osteogenesis. Calcium phosphate (CaP) bioceramics, including hydroxyapatite (HA) and biphasic calcium phosphates (BCPs), have been extensively used in clinical bone defect filling due to their good osteoinductivity and biodegradability. Here, for the first time, we designed and fabricated two porous CaP bioceramic granules with core-shell structures, named in accordance with their composition as BCP@HA and HA@BCP (core@shell). The spherical shape and the porous structure of these granules were achieved by the calcium alginate gel molding technology combined with a H2O2 foaming process. These granules could be stacked to build a porous structure with a porosity of 65-70% and a micropore size distribution between 150 and 450 μm, which is reported to be good for new bone ingrowth. In vitro experiments confirmed that HA@BCP bioceramic granules could promote the proliferation and osteogenic ability when cocultured with bone marrow mesenchymal stem cells, while inhibiting the differentiation of RAW264.7 cells into osteoclasts. In vivo, 12 weeks of implantation in a critical-sized femoral bone defect animal model showed a higher bone volume fraction and bone mineral density in the HA@BCP group than in the BCP@HA or pure HA or BCP groups. From histological analysis, we discovered that the new bone tissue in the HA@BCP group was invading from the surface to the inside of the granules, and most of the bioceramic phase was replaced by the new bone. A higher degree of vascularization at the defect region repaired by HA@BCP was revealed by 3D microvascular perfusion angiography in terms of a higher vessel volume fraction. The current study demonstrated that the core-shell structured HA@BCP bioceramic granules could be a promising candidate for bone defect repair.