To probe the relevance between depressive symptoms and hippocampal volume and its metabolites detected by magnetic resonance imaging (MRI) in depressed patients who were given electro-acupuncture (EA) combined with Fluoxetine before and after treatment. A randomized, controlled trial was conducted. A total of 75 cases of mild or moderate depression were randomly assigned to two groups: the EA group which received EA combined with Fluoxetine; the Fluoxetine group which received Fluoxetine only as the control. The 17-item Hamilton Scale for Depression (HAMD) was used to assess the depression level. The relevance between the changes of the hippocampal volume and its metabolites, including N-acetyl aspartate (NAA)/creatine (Cr) and choline containing compounds (Cho)/Cr, and the reduction rate of the HAMD score before and after treatment of the two groups were analyzed. At the end of the treatment, the therapeutic response rates were not statistically different between the two groups (73.53% for the Fluoxetine group and 83.33% for the EA group, respectively). Compared to that of the Fluoxetine group, a significant difference was shown in the EA group in the reduction rate of the HAMD scores (P < 0.05). There was a negative correlation between the therapeutic effect and the HAMD scores before treatment in both groups of patients. There was no significant difference in the hippocampal volume before and after treatment. The NAA/Cr ratio of both groups increased after treatment, with the EA group increasing more. There was a negative correlation between the rate of change of the NAA/Cr after treatment and the HAMD scores before treatment in the two groups. In the Fluoxetine group, the Cho/Cr ratio showed no significant difference before and after treatment, which had no relevance with the HAMD scores before treatment either. Meanwhile, in the EA group, the Cho/Cr ratio showed a significant difference before and after treatment, which also had a positive relevance with the HAMD scores before treatment. There was a significant improvement in the hippocampal metabolites in depressed patients who treated by EA combined with Fluoxetine. Those differences showed relevance with the HAMD scores before treatment.