Background: The anterior cingulate cortex (ACC) plays an important role in the neuropathology of major depressive disorder (MDD). So far, the effect of local cortical alteration on metabolites in multiple subdivisions of ACC has not been studied. We aimed to investigate structural and biochemical changes and their relationship in the pregenual ACC (pgACC), dorsal ACC (dACC) in MDD. Methods: We obtained magnetic resonance spectroscopy (MRS) in two investigated regions for 24 depressed patients and matched controls. In each region, cortical thickness (CTh) was calculated within a template mask based on its MRS voxel. We investigated neurotransmitter concentrations of Glx, N-acetyl aspartate (NAA), and myo-inositol (m-lns) in two investigated regions, as well as their relationships with CTh in depressed individuals and healthy controls. Results: Patients showed significantly lower cortical thickness in dACC compared to controls. Glx in dACC significantly correlated with CTh in healthy controls but not MDD patients, while NAA and CTh in dACC significantly correlated in both groups. A marginal decrease of Glx in pgACC was found in the subgroup of more severely depressive patients, compared to the mildly depressed patients. Limitations: Modest sample size and lack of episodes of depression may limit the generalizability of our findings. Conclusion: Our results indicate an abolished CTh-MRS relation in dACC associated with structural decline but not in pgACC, where acute MRS alterations prevailed. Our study provides the first evidence of a neurochemical basis explaining some of the inter-individual variability in CTh in MDD.