Cognitive and behavioral symptoms of major depressive disorder (MDD) are linked to aberrant changes in the controllability of brain networks. However, previous studies examined network controllability using white matter tractography, neglecting the contributions of gray matter. We aimed to examine differences in the controllability of morphometric networks between patients with MDD and demographic-matched healthy controls and identify the associated neurobiological signatures.

Based on the structural and diffusion MRI data from two independent cohorts, we calculated the controllability of morphometric similarity networks for each participant. A generalized additive model was used to investigate the case–control differences in regional controllability and their cognitive and behavioral associations. We investigated the associations between imaging-derived controllability and neurotransmitters, brain metabolism, and gene transcription profiles using multivariate linear regression and partial least squares regression analyses.

In both cohorts, depression-related abnormalities of morphometric network controllability were primarily located in the prefrontal, cingulate, and visual cortices, contributing to memory, sensation, and perception processes. These abnormalities in network controllability were spatially aligned with the distributions of serotonergic transmission pathways as well as with altered oxygen and glucose metabolism. In addition, these abnormalities spatially overlapped with differentially expressed genes enriched in annotations related to protein catabolism and mitochondria in neuronal cells and were disproportionately located on chromosome 22.

Collectively, neuroimaging evidence revealed aberrant morphometric network controllability underlying MDD-related cognitive and behavioral deficits, and the associated genetic and molecular signatures may help identify the neurobiological mechanisms underlying MDD and provide feasible therapeutic targets.