Irritable bowel syndrome (IBS) is one of the most common gastrointestinal disorders, with diarrhea predominant IBS (IBS-D) as the most common subtype. Increasing evidence reported that the gut microbiota-mediated serotonin pathway plays a crucial role in the pathogenesis of IBS-D. In this study, potential herbal medicine, plant extracts and its monomers that can be employed as the candidate molecules for IBS-D through gut microbiota-mediated serotonin pathway were reviewed. The bacteria indigenous to gut microbiota regulates serotonin pathway, mainly increasing tryptophan hydroxylase (TPH) and decreasing serotonin reuptake transporter (SERT), by activating cyclooxygenase/prostaglandin E2 (COX/PGE2) signaling. It further accelerated gastrointestinal motility and visceral hyperalgesia. Herbal medicine prescription including Tongxie yaofang and Shugan decoction, as well as some monomers of flavonoid and polyphenol compounds can be regarded as the potential agents for IBS-D. The predominate mechanisms were related to regulating serotonin pathway by driving on the specific bacterial abundance (such as Firmicutes and Bacteroidetes). However, there are few reports on which specific bacteria species play a regulatory role in serotonin pathway, and most of these effective agents were only evidenced by preclinical studies. We hope this review will provide some useful directions for the treatment strategy of IBS-D.