The extraction of a non-restorable tooth, required due to severe caries, periodontitis, or trauma, is a common precursor to dental implantation. Following tooth extraction, physiological bone resorption occurs, and even infections can disrupt the immune microenvironment, further exacerbating bone loss. Some approaches with sophisticated antibacterial and immunomodulatory functions are required to prevent infection and orchestrate favorable tissue regeneration. Herein, guanidylated carbon dots (PG-CDs) with stable physicochemical properties and antibacterial–immunomodulatory functions were synthesized via a controllably hydrothermal method using citric acid and polyhexamethylene guanidine (PHMG) as precursors. PG-CDs possessed uniform spherical morphology, and surface functional groups including –NH2 and guanidyl moieties. PG-CDs displayed potent efficacy against a broad spectrum of bacteria containing oral bacteria and their biofilms via membrane disruption, coupled with high stability and little risk of resistance development. The PG-CDs possessed biocompatibility and effectively promoted a pro-regenerative microenvironment by accelerating osteogenic differentiation and guiding macrophage polarization towards the M2 phenotype. In vivo results further implied that PG-CDs effectively enhanced bone regeneration, effectively reduced oral pathogenic bacterial load, and facilitated extraction socket healing. Collectively, these findings suggest that PG-CDs represent a promising nanomedicine for maintaining alveolar bone height post-extraction and offer an effective therapeutic strategy for bone tissue regeneration.