In clinics, repairing bone tissue with methicillin-resistant Staphylococcus aureus (MRSA) infections and bone defects remains a remarkable challenge. This study designs new core-shell composites of PMP/PVA (Fe3O4@APNs based on magnesium phosphate cement/Fe3O4@APNs-VAN-PLGA microspheres-agarose hydrogel). With Fe3O4@APNs (Phytic acid dodecasodium exfoliated BPNs (APNs) modified with Fe3O4) as an enhanced microwave (MW) sensitizer, the PMP/PVA system exhibits outstanding MW thermal performance. Under MW irradiation, the PMP/PVA exerts dual antibacterial activity through the MW thermal effect (MTE, quickly increased to 68.7 ± 2.4 °C in 5 min at 2.45 GHz, 10 W/cm2) and MW-triggered chemotherapy (CTH, in vitro: 99.98 ± 0.02 % (MRSA), 99.43 ± 0.73 % (E. coli); in vivo: 99.98 ± 0.02 %), which possesses antibacterial ability in vitro and anti-infective effects in vivo with low toxicity and side effects. In addition, PMP/PVA possesses biodegradability with Ca2+, Mg2+, and PO43− released, which not only facilitates the proliferation and osteogenic differentiation of rat bone marrow mesenchymal stem cells (BMSC) in vitro but also promotes new bone formation for bone defect sites with chronic osteomyelitis in vivo (the implantations were gradually replaced with a large area of new bone without apparent cortical reactions). Therefore, PMP/PVA with dual antibacterial activity, osteogenic performance, and low toxicity ability can potentially repair bone tissue with MRSA infections and refractory bone defects. The proposed system is promising for bone tissue repair of chronic osteomyelitis with bone defects.