White matter (WM) abnormalities are implicated in major depressive disorder (MDD), yet the organization of white matter morphometric similarity networks (WM-MSNs) – which capture interregional similarity in voxel-wise WM morphology – and the transcriptional mechanisms associated with their disruption remain insufficiently understood.

Using T1-weighted MRI from a large multisite sample (1,154 individuals with MDD and 1,026 healthy controls), we constructed individualized WM-MSNs. Group differences were assessed at the edge, global, and nodal levels. To identify molecular pathways underlying these alterations, nodal abnormalities were linked to regional gene expression profiles from the Allen Human Brain Atlas using spatially informed transcriptomic association, followed by functional, cell-type-specific, and developmental enrichment analyses.

MDD showed distributed but selective reorganization of WM-MSNs. Network-based statistics revealed two significant components, with 118 edges exhibiting increased morphometric similarity and 45 showing decreased similarity. Globally, MDD demonstrated higher small-worldness, clustering coefficient, global efficiency, and local efficiency, together with shorter characteristic path length. Nodal disruptions were concentrated in major commissural and association tracts – including the corpus callosum, cingulum, uncinate fasciculus, and tapetum. Transcriptomic integration indicated enrichment for gene signatures related to oligodendrocyte function, myelination, lipid metabolism, axonal organization, and cellular stress-related molecular processes, with implicated genes showing broad developmental-stage expression.

MDD is associated with robust alterations in individualized WM-MSNs that converge with transcriptional signatures linked to myelination, metabolic processes, axonal structure, and cellular stress, linking macroscale network disruption to underlying molecular architecture and providing cross-scale insights into WM pathology in depression.