ABSTRACTThe keystone pathogen Porphyromonas gingivalis (P.g.) is responsible for cementum resorption in periodontitis; however, the mechanism involved in it remains unclear. Sirtuin 3 (Sirt3) is a NAD+‐dependent protein deacetylase contributing to mitochondrial homeostasis and various cell functions. In this study, the expression of Sirt3 in cementoblasts was found to be increased during cementoblast mineralisation and cementum development, while it decreased gradually under P.g. infection in a multiplicity of infection‐dependent manner. Compared with wild type mice, the Sirt3 knockout mice showed less cellular cementum and lower mineralisation capacity with decreased expression of Runx2 and OCN in cementoblasts. Sirt3 inhibition by 3‐TYP or Sirt3 silencing by lentivirus infection both confirmed the impaired cementogenesis. Conversely, honokiol (HKL) was simulated to bind Sirt3 and was applied to activate Sirt3 in cementoblasts. HKL‐mediated Sirt3 activation facilitated cementoblast mineralisation and rescued P.g.‐suppressed cementoblast mineralisation markedly. Superoxide dismutase 2 (SOD2), the downstream molecule of Sirt3, showed a similar expression pattern to Sirt3 under different conditions. Silencing of SOD2 was demonstrated to restrain cementoblast mineralisation. The pan acetylation was detected to decrease under Sirt3‐upregulating conditions and increase under Sirt3‐downregulating conditions. The binding of Sirt3 and SOD2 in cementoblasts was also verified. Furthermore, SOD2 acetylation and specific SOD2‐K68 acetylation were found to be upregulated under P.g. or Sirt3 silencing conditions and downregulated by HKL stimulation. Moreover, K68Q mutation simulating acetylation decreased cementoblast mineralisation, while K68R mutation simulating deacetylation increased it. Altogether, Sirt3 deacetylates SOD2 via K68 to orchestrate P.g.‐perturbed cementogenesis, and HKL is a Sirt3‐targeted treatment candidate.