To explore the central molecular biological basis of depression with stagnation of liver qi and spleen deficiency syndrome in rats.Methods:The chronic unpredictable mild stress (CUMS) method was used to establish the model.Rat's brain information was scanned with functional magnetic resonance imaging (fMRI).The amplitude of the low-frequency fluctuations (ALFF) and the abnormal brain region in regional homogeneity (Reho) of rats in normal group and depression with stagnation of liver qi and spleen deficiency syndrome group were calculated and analyzed by SPM8.High performance liquid chromatography（HPLC）was used to detect the monoamine neurotransmitter change of the close related brain region.Sini Powder was used to confirm the biological basis from the perspective of counterevidence.Results:Both ALFF and Reho in the hypothalamus were decreased.The contents of dopamine (DA),serotonin (5-HT),and 5 hydroxyindole acetic acid (5-HIAA) and norepinephrine (NE) were reduced significantly (P<0.05).The content of 5-HT of Sini Powder group increased more significantly than that of normal group (P<0.05).There was improvement tendency in the DA,5-HIAA,and NE (P>0.05).Conclusion:The 5-HT,5-HIAA,NE,DA in the hypothalamus were parts of the central biological basis of depression with stagnation of liver qi and spleen deficiency syndrome.