This study demonstrates a novel, simple way of synthesizing bone morphogenetic protein (BMP)-loaded hydroxyapatite (HA) microspheres for enhanced bone regeneration. To accomplish this, calcium phosphate cement (CPC) microspheres, consisting of α-TCP and TTCP powders, were prepared using water-in-oil (W/O) emulsion, followed by treatment at 37 °C for 3 days to convert the CPC to HA. The BMP-loaded HA microspheres with a well-defined spherical shape had a highly porous structure, which was created by the entanglement of precipitated HA crystals with a needle-like morphology. The unique porous structure with the bone mineral-like HA phase resulted in a considerable improvement in in vitro biocompatibility. In addition, the bone regeneration ability of the HA microspheres was significantly enhanced by BMP loading, which was examined by in vivo animal testing using a rabbit vertical guided bone regeneration model.