Serotonin (5-HT) is a highly conserved neurotransmitter and widely expresses in various tissues of mammals. Extensive expression of 5-HT in cerebral cortex and synapses acts as an inhibitory neurotransmitter. 5-HT in peripheral tissues involves in many physiological processes such as muscle contraction, blood pressure regulation and platelet aggregation. Recently, researchers have found that in addition to the central and peripheral nervous system, 5-HT was widely expressed in the digestive system and played an important role in the physiological and pathological processes of digestive system. This review intends to explore the role of 5-HT in digestive patho-physiology and regulatory mechanism as well as 5-HT-based therapeutics for the treatment of digestive diseases.