Objective This study aimed to evaluate the bone integration performance of antibacterial carbon dot (CD)-modified polyether ether ketone (PEEK) in infectious bone defect environments. Methods Guanidine-based CDs (G-CDs) prepared by the melting method combined with dialysis purification were used to modify PEEK implants using polyvinyl butyraldehyde (PVB) by the soaking-drying method (PEEK/PVB-G-CDs). SD rats were divided into the following groups: (1) PEEK-implanted uninfected (PEEK(-)), (2) PEEK/PVB-G-CDs-implanted uninfected (PEEK/ PVB-G-CDs(-)), (3) PEEK-implanted infected (PEEK(+)), and (4) PEEK/PVB-G-CDs-implanted infected (PEEK/PVB-G-CDs(+)). A hole (diameter 2 mm, depth 5 mm) was drilled at the lateral condyle of the vertical femur in all rats to simulate a bone defect. Rats in the PEEK(-) and PEEK/PVB-G-CDs(-) groups without infection were injected with 30 μL physiological saline into the bone marrow cavity, and rats in the PEEK(+) and PEEK/PVB-G-CDs (+) groups with infection were injected with 30 μL MRSA bacterial suspension (1.5 × 10⁴ colony-forming units/mL) into the bone marrow cavity. The implantation site was observed using animal-specific X-ray examination at 0, 2, and 4 weeks after implantation, and the bone tissue characteristics of the implantation site were evaluated by micro computed tomography (CT) at 6 weeks after surgery. The bone implantation sites in each group of rats were examined by bacterial culture of bone marrow and hematoxylin and eosin staining, Toluidine blue, Goldner trichrome, and immunohistochemical staining. Results X-ray, Micro-CT, bacterial culture of bone marrow, and histopathological analysis confirmed no signs of infection in the PEEK(-) and PEEK/PVB-G-CDs(-) groups and the implants were integrated with the bone defects. Rats in the PEEK/PVB-G-CDs(+) group showed signs of antibacterial activity that effectively controlled the osteomyelitis caused by MRSA and achieved bone integration, while rats in the PEEK(+) group failed to achieve bone integration because of persistent infection. Immunohistochemical staining confirmed lower levels of anti-inflammatory factors such as IL-4 and IL10 in the PEEK(+) group, and stronger expression of pro-inflammatory factors such as IL-6 and TNF-α compared with the other three groups, indicating that G-CD-modified PEEK inhibited MRSA infection, regulated inflammation levels in the local microenvironment, and promoted bone integration at the site of bone defects. Conclusions Antibacterial G-CDs modified PEEK exhibits excellent bone integration performance, providing a candidate strategy for future clinical treatment of infectious bone defects.