Background Drug-resistant epilepsy (DRE) is associated with distributed laminar disruptions due to cytoarchitectonic pathologies, which may be characterized by multimodal MRI approaches such as morphometric similarity networks (MSNs). However, the genetic and histological underpinning of MSN alterations in DRE remains poorly understood, hampering its clinical application.Methods We enrolled 60 patients with DRE and 23 controls, acquiring T1 and diffusion spectrum imaging data with a 3.0T GE SIGNA Premier scanner. Morphometric similarity networks (MSNs) were constructed and analyzed to identify microstructure similarity differences between patients and controls. Subsequently, patient-specific MSN alteration patterns were associated with gene expression using the GAMBA tool, and layer-specific neuronal signature mapping were also applied. During these analyses, sex and age were adjusted as covariates and multiple comparisons corrections were applied when appropriate.Findings We observed widespread MSN changes in patients with DRE and identified five distinct MSN alteration patterns. Major patterns presented pattern-specific associations with expressions of epilepsy-related genes, particularly involving the mTOR pathway. Histological analysis confirmed the presence of cortical microstructure changes in areas with MSN alterations and revealed cellular abnormalities matching the aforementioned genetic risks.Interpretation Our findings highlight the potential of quantifying laminar-related microstructure integrity using MSN to uncover the cytoarchitectonic changes in the pathophysiology of DRE. This approach may facilitate the identification of genetic and histological underpinnings of MSN alterations in DRE, ultimately aiding in the development of targeted therapeutic strategies.Fundings The National Natural Science Foundation of China, the Ministry of Science and Technology of the People's Republic of China, and the Beijing Municipal Health Commission.Copyright (c) 2023 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).