Abstract The treatment of bone defect after bone tumor resection is a great challenge for orthopedic surgeons. It should consider that not only to inhibit tumor growth and recurrence, but also to repair the defect and preserve the limb function. Hence, it is necessary to find an ideal functional biomaterial that can repair bone defects and inactivate tumor. Magnetic nanoparticles (MNPs) have its unique advantages to achieve targeted hyperthermia to avoid damage to surrounding normal tissues and promote osteoblastic activity and bone formation. Based on the previous stage, we successfully prepared hydroxyapatite (HAP) composite poly(lactic-co-glycolic acid) (PLGA) scaffolds and verified its good osteogenic properties, in this study, we produced an HAP composite PLGA scaffolds modified with MNPs. The composite scaffold showed appropriate porosity and mechanical characteristics, while MNPs possessed excellent magnetic and thermal properties. The cytological assay indicated that the MNPs have antitumor ability and the composite scaffold possessed good biocompatibility. In vivo bone defect repair experiment revealed that the composite scaffold had good osteogenic capacity. Hence, we could demonstrate that the composite scaffolds have a good effect in bone repair, which could provide a potential approach for repairing bone defect after bone tumor excision.