Evidence of structural and resting-state functional brain abnormalities in MDD has been inconsistent. We conducted the first multimodal meta-analysis of voxel-based morphometry (VBM) and amplitude of low-frequency fluctuation (ALFF) studies in first-episode drug-naïve MDD patients. 15 VBM data setsand 11 ALFF data sets were included. A multimodal meta-analysis was used to highlight brain regions with both structural and functional abnormalities. The multimodal meta-analysis identified conjoint structural and functional differences in the left lateral orbitofrontal cortex and right supplementary motor area. Dissociated anatomical and functional brain abnormalities in MDD were also observed. Meta-analysis revealed in MDD a complex pattern of conjoint and dissociated structural and functional brain abnormalities in brain regions involved in cognition and emotional processing.