Periodontitis is a common inflammatory gum disease that destroys the periodontal tissue. Gastrodin (GAS) is the predominant bioactive component of Gastrodia elata Blume and exhibits anti-inflammatory, anti-apoptotic and antioxidant effects in various diseases, including bone-related diseases. The aim of the present study was to investigate whether GAS could protect lipopolysaccharide (LPS)-treated human periodontal ligament stem cells (hPDLSCs) against injury and inflammation, and to determine the potential underlying mechanisms. hPDLSCs were treated with LPS and GAS, alone or in combination, and cell viability, inflammation, oxidative stress levels and apoptosis were analyzed using a Cell Counting Kit-8 assay, ELISA assay, western blotting and flow cytometry, respectively. The osteogenic differentiation capacity was evaluated using an alkaline phosphatase (ALP) assay and Alizarin Red S staining. Sirtuin 3 (SIRT3) was silenced in cells treated with LPS and GAS to verify the involvement of SIRT3 in the effects of GAS. The results demonstrated that LPS-induced decrease in cell viability was rescued by treatment with 1, 10 or 50 µM GAS. The LPS-induced production of proinflammatory cytokines and increased level of oxidative stress were also inhibited following treatment with 50 µM GAS. Furthermore, GAS significantly promoted ALP activity, increased the number of mineralized nodules and increased the expression of proteins involved in osteogenic differentiation, including ALP, Runx2, osteocalcin and osteopontin, after osteoinduction, which were all downregulated following LPS stimulation. In addition, GAS prevented LPS-induced cell apoptosis and restored the imbalance of anti-apoptotic and proapoptotic proteins in hPDLSCs. In addition, SIRT3 knockdown significantly inhibited the protective effect of GAS on LPS-induced hPDLSC injury. In summary, the findings form the present study suggested that GAS may protect hPDLSCs from LPS-induced inflammation, apoptosis and oxidative stress, as well as promote their osteogenic differentiation. The effect of GAS on the osteogenic differentiation of hPDLSCs may therefore depend on the upregulated expression of SIRT3.