Periodontitis is a chronic inflammatory disease caused by dental plaque, which leads to tooth loosening and shifting or even tooth loss. Current treatments, including mechanical debridement and antibiotics, often fail to eradicate recalcitrant biofilms and mitigate excessive inflammation. Moreover, these interventions can disrupt the oral microbiome, potentially compromising long-term treatment outcomes. To address these limitations, an injectable nanoenzyme hydrogel composed of a dopamine (DA)-modified hyaluronic acid (HA) scaffold and a graphdiyne-iron (GDY-Fe) complex, named GDY-Fe@HA-DA, exhibits excellent tissue adhesion, self-healing, antibacterial properties, and biocompatibility. Under near-infrared laser irradiation, GDY-Fe@HA-DA effectively eradicates a variety of pathogens, including Escherichia coli, Staphylococcus aureus, and Porphyromonas gingivalis, through a synergistic combination of chemodynamical and photothermal therapies. The hydrogel's efficacy is further validated in both bacterial-infected skin wounds and rat periodontitis models. It effectively alleviates the inflammatory environment and promotes wound healing and periodontal tissue recovery. This findings highlight the potential of GDY-Fe@HA-DA as a promising therapeutic material for periodontitis and other tissue injuries.