To systematically investigate the different effects of large, medium and small dose of Xiaoyao Powder on gene expression profile in stomach tissue of rats with the syndrome of liver-depression and spleen-deficiency induced by chronic immobilization stress and to study the anti-stress regulatory mechanism of the three different doses at the whole genome. Methods:The rat whole genome expression chips (Agilent) were used to detect the differences of gene expression in the Stomach of the rat model with the syndrome of liver-depression and spleen-deficiency induced by 21-day chronic immobilization stress(3 hours per day) in normal group, model group and Xiaoyao Powder groups (large, medium and small dose,respectively), and any differential gene expression profiles between groups were recognized and selected. Then the differential gene expression profiles were analyzed through gene ontology and signal pathway 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) had 597，1216，817，924 function gene groups respectively, and signal pathways had 27，60，41，59 respectively. Conclusion:The syndrome of liver-depression and spleen-deficiency has the background of differentially expressed genomics in stomach. The large, medium and small dose of Xiaoyao Powder all have certain intervention effects on multiple stomach differentially expressed genes, the signal pathways and the biological processes whose functions are both changed. The result shows the medium dose of Xiaoyao Powder is better than the large and small dose.