Purpose This study aims to evaluate the bone integration performance of antibacterial carbon dot modified polyether ether ketone (PEEK) in infectious bone defect environments Methods Guanidine based carbon dots (G-CDs) prepared by melting method combined with dialysis purification were applied to modify PEEK implants using polyvinyl butyraldehyde (PVB) by soaking-drying method (PEEK/PVB-G-CDs). The SD rats were divided into: (1) PEEK implanted uninfected group (PEEK (-) group), (2) PEEK/PVB-G-CDs implanted uninfected group (PEEK/PVB-G-CDs (-) group), (3) PEEK implanted infected group (PEEK (+) group), (4) PEEK/PVB-G-CDs implanted infected group (PEEK/PVB-G-CDs (+) group). A hole with a diameter of 2 mm and a depth of 5 mm at the lateral condyle of the vertical femur were drilled on each group of rats to simulate a bone defect. The PEEK (-) and PEEK/PVB-G-CDs (-) groups without infection were injected 30 μL physiological saline into the bone marrow cavity of each rat. The PEEK (+) and PEEK/PVB-G-CDs (+) groups with infection were injected 30 μL MRSA bacterial suspension (1.5 × 104CFU/mL) into the bone marrow cavity of each rat. At 0, 2, and 4 weeks after implantation, animal specific X-ray was used to observe the implantation site of each group of rats. After 6 weeks of surgery, Micro CT was used to evaluate the bone tissue characteristics of the implantation site. Bacterial culture of bone marrow, Hematoxylin eosin staining, Toluidine blue staining, Goldner trichrome staining, and immunohistochemical staining were used to analyze the bone implantation sites of each group of rats. Results (1) X-ray, Micro CT, bacterial culture of bone marrow, and histopathological analysis confirmed that there was no infection in the PEEK (-) and PEEK/PVB-G-CDs (-) groups. The implants were integrated with bone defects. The PEEK/PVB-G-CDs (+) group exerted antibacterial activity to effectively control osteomyelitis caused by MRSA and achieved bone integration, while the PEEK (+) group was unable to achieve bone integration due to persistent infection. (2) Immunohistochemical staining evaluation confirmed that the PEEK (+) group showed lower levels of anti-inflammatory factors such as IL-4 and IL-10, as well as stronger expression of pro-inflammatory factors such as IL-6 and TNF-α compared to the other three groups, indicating that G-CDs modified PEEK can inhibit MRSA infection, regulate the inflammatory level of the local microenvironment, and promote bone integration at the site of bone defects. Conclusions Antibacterial carbon dots modified PEEK exhibits excellent bone integration performance, providing a candidate strategy for future clinical treatment.