Traditional Chinese medicine (TCM) has been commonly used for irritable bowel syndrome (IBS). Syndrome differentiation is one of the important characteristics of TCM. To assess the application and basic characteristics of syndrome differentiation in randomized controlled trials (RCTs) of Chinese herbal medicine for IBS, we performed this paper. We conducted electronic searches in main Chinese and English databases till March 2012. A total of 735 RCTs involving 67,784 IBS participants were included. 224 (30.5%) studies applied syndrome differentiation. The major syndromes of IBS patients were the syndrome of liver stagnation and spleen deficiency (56.8%), spleen-stomach weakness (49.4%), spleen-kidney yang deficiency (48.1%), and cold and heat in complexity (29.6%). Herbal formulas were prescribed based on syndrome differentiation in 202 studies. Chinese patent medicine was more commonly used in studies that only enrolled patients with a specific syndrome. 15 studies compared the therapeutic effect among different syndromes, of which 6 studies showed that there were significant differences among different syndromes. The low use of TCM syndrome differentiation in randomized trials of Chinese herbal medicine for IBS results in the poor pertinence of treatment. TCM syndrome differentiation should be used in further studies at the stage of recruitment, treatment, and data analyses.