3D porous scaffolds based on biodegradable polymers are one of the materials for bone tissue regeneration. In this study, a porous scaffold was prepared using a solvent casting/particulate leaching method that used polycaprolactone (PCL) and hydroxyapatite (OceanBone-HAp) extracted from a marine plankton exoskeleton to achieve excellent bone regeneration. In this study, the morphology and physicochemical properties of the PCL/OceanBone-HAp scaffolds were evaluated using scanning electron microscopy, X-ray diffraction, and porosity analysis. The results confirmed the porous structure of the scaffold and removal of the solvent and porogen particles. In vitro test results revealed superior cell adhesion, proliferation, and viability of PCL/OceanBone-HAp scaffolds compared to PCL scaffolds alone. The enhanced alkaline phosphatase activity and expression of bone morphogenetic protein 2, collagen type I α 1, osteocalcin, and bone sialoprotein in the PCL/OceanBone-HAp scaffolds were confirmed through ALP and real-time polymerase chain reaction assays. Moreover, in vivo experiments using a rabbit calvarial defect model showed that the PCL/OceanBone-HAp scaffold exhibited enhanced bone regeneration compared to the PCL scaffold. Therefore, the PCL/OceanBone-HAp scaffold is a promising scaffold for bone repair.