Xiaoyaosan is the classic prescription of soothing the liver and invigorating the spleen, which is widely used in clinical departments, especially syndrome of stagnation of liver qi and spleen deficiency. For long times, there is a lot of researches about the inner link between the regulating effect of Xiaoyaosan and the mechanism of syndrome of liver depression and spleen deficiency. This paper starts from the molecular mechanism, and discusses the thought in prescription and syndrome of Xiaoyaosan, hoping to provide the thinking and method to the study of prescription and syndrome including Xiaoyaosan and syndrome of stagnation of liver qi and spleen deficiency.