Objective This study identified the inhibitory effects of Yinqiaosan (YQS) and its disassembled prescriptions on improvement of clinical symptoms of viral influenza such as fever relieve, prevention complications of viral influenza and evaluation clinical safety of YQS on viral influenza treatment, a clinical trial was performed on 124 cases of influenza patients using randomized controlled trial. Understood the active ingredients and functional drug combination of YQS, even its mathematical quantitative law among Chinese herbals, leaded great challenges for simplification of YQS prescription, and provided further chances for exploration on YQS's multiple targets against influenza. Methods A randomized, single blind clinical trial design was used. 124 patients with influenza aged 13-60 years undergoing classical influenza symptoms diagnosed in fever clinic of Emergency department in Guangdong Provincial Hospital of Chinese Medicine were randomly assigned to YQS whole recipe group (n = 43), YQS sovereign and minister drugs group (n = 41), and YQS sovereign and assistant drugs group (n = 40), and treated for 5 days respectively. The main symptoms of influenza such as fever, runny or snuffle nose, sore throat, coughing, muscle pain, weakness/fatigue, headache and chills, and safety of those prescriptions were quantified by evaluated scale beginning at drugs administration of YQS. PASW Statistics18.0 software was used for all data analyses. Results There was no significant difference (P>0.05) among three groups of patients' age, gender, onset of disease and symptoms before treatment, indicating the comparability of three groups. The results of variance analysis in fever relief time shows a significant time trend between YQS whole recipe group and YQS sovereign and assistant drugs group (P<0.05), and between YQS sovereign and minister drugs group and YQS sovereign and assistant drugs group (P<0.05). The repeated measures analysis of variance confirmed those results at before, the first day, the third day and fifth day after drug administration (P<0.05). Variance of each quantified symptoms at 1, 3 and 5 days of treatment among three groups were analyzed. At day 3 and day 5, the improvement of symptoms in sovereign and minister, equally with whole recipe group (P>0.05), were shown significantly difference, compared with th e sovereign and assistant group (P>0.05). The scores of influenza symptoms were marked difference among three groups in day 3 and day 5 time point (P<0.05). There was no significantly difference between the whole recipe group and sovereign and minister group on relieving the main symptoms of influenza such as fever, runny or snuffle nose, sore throat, coughing, muscle pain, weakness/fatigue, headache and Chills et al. (P>0.05). However, the quantified symptoms in those two groups are superior to the sovereign and assistant group (P<0.05). All of the three groups showed little effect on relieving cough. The response rate and complete remission rates in the whole recipe group and the sovereign and minister group are better than the sovereign and assistant group (P<0.05). No severe adverse reaction were observed in three groups. Conclusion 1. YQS and its disassembled prescriptions can provide an effective treatment to cure influenza, all of three prescriptions can relieve the clinical symptoms of influenza. 2. The curative effects of influenza by sovereign and minister group was equal to whole recipe group, but better than the sovereign and assistant group. 3. There was no obviously difference in response rate and complete remission rates between the whole recipe group and the sovereign and minister group, but contrarily there was significantly difference between them and sovereign and assistant group. 4. YQS and its disassembled prescriptions are safe to patients with influenza, no severe adverse reaction were observed in three groups.