Agarwood, as a precious medicinal material with distinctive characteristics from Hainan, has been shown in recent studies to possess significant anti-inflammatory and antibacterial properties. With the rapid growth in public recognition of health concepts, oral health has garnered increased attention. The main focus of this study is the impact of agarwood extracts on the oral-gut axis microbiota. The relationship between the oral and gut microbiota is closely intertwined, where oral microbiota can directly colonize the intestine via saliva and other means, altering the original microbial composition of the gut and leading to dysbiosis. For instance, Porphyromonas gingivalis significantly increases in patients with gingivitis and periodontitis, as it can tolerate the acidic environment of the stomach and colonize the intestines through the gastric barrier. Therefore, oral health can affect intestinal health. Additionally, oral lesions are evident in patients with intestinal inflammation; such patients, like those with IBD, exhibit a significant accumulation of oral bacteria in the intestines. Although IBD primarily affects the intestines, its extraintestinal symptoms, often prominently displayed, include oral manifestations. Hence, intestinal health can also influence oral health. Agarwood extracts inhibit pathogenic oral microbiota, impedes their colonization in the intestine, and consequently reduces the likelihood of inflammatory bowel disease.. This article, by introducing the microbiota of periodontitis and the pathogenesis of inflammatory bowel disease, along with extraintestinal symptoms, the preventive and inhibitory mechanisms of agarwood extract on the associated microbiota are analyzed, providing new insights for the treatment of such patients. It underscores the importance of maintaining oral hygiene and preventing oral diseases as well.