OBJECTIVE: This study aimed to explore the causal relationship between brain cortical and subcortical structures and major depressive disorder (MDD) using the Mendelian Randomization (MR) method. METHODS: Single nucleotide polymorphisms (SNPs) were used as instrumental variables to analyze subcortical brain volume, cortical thickness, and surface area as exposure factors, with MDD as the outcome. Multiple sensitivity analyses were conducted to validate the robustness of the results. RESULTS: MR analysis showed a significant negative correlation between subcortical brain volume and MDD. Specifically, the volumes of the caudate nucleus, hippocampus, intracranial region, and thalamus were inversely associated with the risk of MDD, indicating that larger subcortical brain volumes were linked to a lower risk of MDD. The thickness of the entorhinal cortex was also negatively correlated with MDD. At the same time, certain cortical regions showed significant positive correlations between surface area and MDD. Increased thickness of the entorhinal cortex and increased surface areas of the isthmus of the cingulate gyrus, middle temporal gyrus, and precuneus were associated with a higher risk of MDD. The sensitivity analyses revealed no significant heterogeneity or horizontal pleiotropy, and the results were consistent across different methods, confirming their robustness. CONCLUSION: The study found that increased volumes of the caudate nucleus, hippocampus, internal capsule, and thalamus in subcortical brain regions and increased thickness of the entorhinal cortex in cortical regions were associated with a reduced risk of MDD, while increased surface areas of the isthmus of the cingulate gyrus, middle temporal gyrus, and precuneus in cortical regions were linked to an elevated risk of MDD.