Objective:To observe the clinical effect of Wenzhen Yunqi recipe in treating patients of chronic fatigue syndrome with negative emotion . Methods153 subjects were randomly divided into the health group(50 cases),treatment group(51 cases) and control group(52 cases). The health group was received any treatment,the treatment group was treated with Wenzhen Yunqi Recipe and the control group was treated with Chinese patent medicine Xiaoyao pill,with a course of 3 months. The score changes of fatigue scale-14 (F-14),Hamilton anxiety scale (HAMA),Hamilton depression scale (HAMD) and health status questionnaire (SF-36) score were observed,as well as the regulating effect on hydrogen proton magnetic resonance spectroscopy (1H-MRS) in bilateral hippocampal area.  Results:①3 cases fell off during the trial(1 case in the treatment group and 2 cases in the control group)；finally 150 cases completed the trial,50 cases in each group. ②Comparison of before and after treatment,the differences on the score of F-14,HAMD and HAMA in both groups were statistically significant(P<0.05)；after treatment,the differences on the score of F-14,HAMD and HAMA between groups were statistically significant,and the effects on fatigue and negative emotion in the treatment group were better than those in the control group(P<0.05) ③Comparison of before and after treatment,the differences on the five dimensions scores in SF-36(body function,general health,life vitality,emotional role and psychological health) in the treatment groups were statistically significant(P<0.05)；the differences on the two dimensions scores(life vitality,psychological health)in the control groups were statistically significant(P<0.05).After treatment,the differences on the five dimensions scores in SF-36(body function,general health,life vitality,emotional role and psychological health)between groups were statistically significant(P<0.05). ④Before treatment,there were statistically significant difference on the ratio of NAA/Cr and Cho/Cr in the left and right hippocampus in the treatment and control groups compared with the health group(P<0.05),but the difference on the ratio of NAA/Cr and Cho/Cr between the treatment and control groups was not statistically significant(P>0.05). Comparison of before and after treatment,the ratio of NAA/Cr in the left and right hippocampus in the treatment group was significantly increased,the ratio Cho/Cr in the left hippocampus was significantly decreased(P<0.05),the difference on the ratio Cho/Cr in the right hippocampus was not statistically significant(P>0.05)；the differences on the ratio of NAA/Cr and Cho/Cr in the left and right hippocampus in the control group were not statistically significant(P>0.05). After treatment,the increase of the NAA/Cr in the left and right hippocampus in the treatment group was more significant than that in the control group,and the decrease of the ratio Cho/Cr in the left hippocampus was more significant than that in the control group(P<0.05).  Conclusion:Wenzhen Yunqi Recipe shows effect in the treatment of chronic fatigue syndrome,which significantly ameliorate the negative emotional and physical fatigue of the patients and improve the quality of life. Its mechanism may be related to regulation of functional metabolism(NAA/Cr、Cho/Cr)in the central hippocampus.