To systematically investigate the effect of Xiaoyao powder on hypothalamus gene expression profile of rats with syndrome of liver-depression and spleen-deficiency induced by chronic immobilization stress and its anti-stress regulatory mechanism at the whole genome. Methods:The rat whole genome expression chips(Agilent) were used to detect gene expression differences in the hypothalamus of the rat model with liver-stagnation and spleen-deficiency syndrome induced by chronic immobilization stress(daily immobilization stress for 3 h for 21 days) in normal group, model group and Xiaoyao powder group(large, medium and small doses) and any different gene expression profiles between groups were recognized and selected.The hypothalamus gene expression profile was studied through gene ontology and signal pathway analyses using bioinformatics. Results:The differential gene expression profiles of model group and Xiaoyao Powder groups (large, medium and small dose) were different. The functions of multiple biological processes and signaling pathways were significantly up-regulated or down-regulated. The significantly-changed biological processes participated by differential gene of the model group and the Xiaoyao Powder groups(Large, medium and small dose) had909,712,516,1322 respectively, and signal pathways had 60,57,41,90 respectively. Conclusion:The liver-stagnation and spleen-deficiency syndrome has the background of differentially expressed genomics in hypothalamus. The large, medium and small doses of Xiaoyao powder all have a certain intervention effect on multiple hypothalamus differentially expressed genes, signal pathway and biological process whose functions are both changed. The result shows the large and medium doses are better than the small dose.