Dracocephalum Moldavica L. (DML), a Chinese traditional medicine rich in flavone compounds (e.g., tilianin), has shown antioxidant and anti-inflammatory potential for alleviating inflammatory disorders. However, the extraction of active ingredients of DML is complex, and these extracts usually act synergistically to treat inflammatory diseases. In this study, the carbon dots derived from DML (T-CDs) were rapidly prepared via the one-pot method and showed good performance in biocompatibility and free radical scavenging capacity. Then, the T-CDs were loaded into the hydrogel and applied to treat periodontitis. The in vivo experiments demonstrated that T-CDs could promote the inflammation resolution of and the alveolar bone reparation in the periodontitis model after periodontal injection. With further investigation, it could be found that T-CDs involved the alternative polarization of macrophage by rebalancing glycolysis and mitochondrial respiration. Overall, it was the first time DML had been used to prepare carbon dots with anti-inflammation. This study provided an effective drug candidate for the treatment of periodontitis and offered an in-depth understanding of the therapeutic mechanism of T-CDs in periodontitis through macrophage immunomodulation.