Background: Although there are some Chinese herbal medicines in treatment of constipation, but no multi-center randomized controlled trials have been carried out to prove their effectiveness. Objective: To evaluate the safety and efficacy of Yunchang Capsule in treatment of functional constipation with deficiency of both qi and yin and internal accumulation of poisonous pathogenic factors syndrome, and to explore the clinical dosage. Design, setting, participants and interventions: A randomized, double-blinded controlled, multicenter trial was conducted. A total of 240 patients with functional constipation from West China Hospital of Sichuan University, Affiliated Hospital of Chengdu University of Traditional Chinese Medicine, Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, the First Affiliated Hospital of Tianjing University of Traditional Chinese Medicine and Fujian Academy of Traditional Chinese Medicine were randomly divided into three groups: low dose group (80 cases), high dose group (80 cases) and control group (80 cases). Patients in the low dose group were treated with two pills (0.35 g/pill) of Yunchang Capsule and one pill of Yunchang Capsule simulant for three times daily; patients in the high dose group were treated with three pills (0.35 g/pill) of Yunchang Capsule for three times daily; and patients in the control group were treated with three pills (0.35 g/pill) of Biantong Capsule for three times daily. The therapeutic course was 14 days. Main outcome measures: Clinical symptoms, syndromes, and adverse effects were observed before and after the treatment, and blood, urine and stool tests, hepatorenal function and electrocardiogram were also examined. Results: Two cases were excluded, eleven cases were lost to follow-up, and there were 234 patients entered to intention-to-treat (ITT) analysis. After the treatment, the therapeutic effects were calculated by full analysis set (FAS) and per-protocol population set (PPS) analysis respectively. The effects on functional constipation in FAS showed the response rates in the low dose, high dose and control groups were 86.25% (69/80), 82.90% (63/76), and 70.52% (55/78) respectively, and PPS analysis showed the response rates were 85.71% (66/77), 83.56% (61/73), and 70.13% (54/77) respectively. There were no significant differences among the three groups (P>0.05). The effects on traditional Chinese medicine syndrome in FAS showed the response rates in the low dose, high dose and control groups were 78.75% (63/80), 69.74% (53/76), and 67.95% (53/78) respectively, and PPS analysis showed the response rates were 77.92% (60/77), 69.87%(51/73), and 67.53% (52/77) respectively. There were also no significant differences among the three groups (P>0.05). No severe adverse events were observed. Conclusion: Both low dose and high dose of Yunchang Capsule are effective and safe in treatment of functional constipation with deficiency of both qi and yin and internal accumulation of poisonous pathogenic factors syndrome.