Background: Irritable bowel syndrome (IBS) is one kind of common functional bowel disease with obscure pathogenesis, and exploration about whole transcriptome profiling in IBS-D is still negligible. Conventional medications have limited effects, which makes focus shifted to traditional Chinese medicine (TCM). Tong-Xie-Yao-Fang, as a classic herbal formula in TCM, is pretty effective and safe for the treatment of diarrhea-predominant irritable bowel syndrome (IBS-D), but the underlying therapeutic mechanism remains unknown. We aim to verify the efficacy and safety of TXYF granule (the formula particles mixed together) in IBS-D and elucidate the gene-level mechanism of IBS-D and therapeutic targets of TXYF granule based on whole transcriptome analysis. Methods/design: This is a randomized, double-blind, and placebo-controlled clinical trial consisting of 2 weeks of run-in period, 12 weeks of treatment period, and 8 weeks of follow-up period. We will enroll 120 participants with IBS-D, who will be randomly assigned to the TXYF granule group and the placebo group, and recruit additional 10 healthy individuals as controls for mechanistic outcome. The two groups respectively take TXYF granule or placebo orally for treatment. The primary outcome is the response rate of IBS-Symptom Severity Score (IBS-SSS). The secondary outcomes include adequate relief (AR), IBS-Quality of Life Questionnaire (IBS-QOL), and long-term efficacy. Mechanistic outcome is the whole transcriptome profiling of the intestinal mucosae from IBS participants before and after the treatment and healthy individuals. Discussion: This trial will prove the effectiveness and safety of TXYF granule with high-quality evidence and provide a penetrating and comprehensive perspective on the molecular mechanism of IBS-D by whole transcriptome analysis, which makes us pinpoint specific biomarkers of IBS-D and therapeutic targets of TXYF.