Phenolic compounds are widely found in natural Chinese medicinal plants and have excellent pharmacological properties, such as antioxidation and anti-inflammation. They are the main pharmacological components of many medicinal Chinese herbs. Oral microbiota, especially its composition and metabolism, is highly related to the balance of oral microecology and plays a key role in the occurrence and development of oral diseases. Recent studies have shown that phenolic compounds of traditional Chinese herbs can prevent and treat oral diseases, such as caries, periodontal disease, and oral mucosal infection, by regulating the composition, metabolites, and virulence of oral microorganisms. This review will summarize and discuss the regulation of phenolic compounds on oral microbes.