We evaluated the effects of paeonol, a phenolic compound of Moutan Cortex, on the tissue inflammation and destruction in experimental periodontitis of rats. The maxillary palatal bony surfaces of 18 rats received injections of lipopolysaccharide (LPS, 5 mg/mL), PBS or LPS-plus-paeonol (40 mg/kg, intra-peritoneal injection) for three days. Five days later, the osteoclasts were examined and compared after tartrate-resistant acid phosphatase staining. In another 36 rats, the experimental periodontitis was induced by placing the ligatures around the maxillary second and mandibular first molars. Seven days later, the periodontal destruction and inflammation in rats with paeonol (40 mg/kg or 80 mg/kg) and those who had no ligature or without paeonol were compared by dental radiography, micro-computerized tomography (micro-CT), and histology. Gingival mRNA expressions of pre-inflammatory cytokines, including IL-1β' IL-6 and TNF-α were also examined. Compared to the effect of the LPS positive control, the paeonol injection significantly reduced the induced osteoclast formation. In ligature-induced periodontitis, the periodontal bone supporting ratio was significantly higher in the ligature-plus-paeonol groups compared to that of the ligature group, although they were still less than those in the non-ligature group. By micro-CT and by histology/histometry, a consistent anti-destructive effect was observed when paeonol was added. Moreover, less amount of inflammatory cell-infiltrated connective tissue area, connective tissue attachment, and mRNA expressions of pro-inflammatory cytokines were presented in the ligature-plus-paeonol groups than those in the ligature group. These results suggested that paeonol might have a protective potential on gingival tissue inflammation and alveolar bone loss during the process of periodontitis by inhibiting pro-inflammatory cytokines.