ObjectiveTo evaluate the intrinsic and extrinsic microstructural factors contributing to atrophy within individual thalamic subregions in multiple sclerosis using in vivo high‐gradient diffusion MRI.MethodsIn this cross‐sectional study, 41 people with multiple sclerosis and 34 age and sex‐matched healthy controls underwent 3T MRI with up to 300 mT/m gradients using a multi‐shell diffusion protocol consisting of eight b‐values and diffusion time of 19 ms. Each thalamus was parcellated into 25 subregions for volume determination and diffusion metric estimation. The soma and neurite density imaging model was applied to obtain estimates of intra‐neurite, intra‐soma, and extra‐cellular signal fractions for each subregion and within structurally connected white matter trajectories and cortex.ResultsMultiple sclerosis‐related volume loss was more pronounced in posterior/medial subregions than anterior/ventral subregions. Intra‐soma signal fraction was lower in multiple sclerosis, reflecting reduced cell body density, while the extra‐cellular signal fraction was higher, reflecting greater extra‐cellular space, both of which were observed more in posterior/medial subregions than anterior/ventral subregions. Lower intra‐neurite signal fraction in connected normal‐appearing white matter and lower intra‐soma signal fraction of structurally connected cortex were associated with reduced subregional thalamic volumes. Intrinsic and extrinsic microstructural measures independently related to subregional volume with heterogeneity across atrophy‐prone thalamic nuclei. Extrinsic microstructural alterations predicted left anteroventral, intrinsic microstructural alterations predicted bilateral medial pulvinar, and both intrinsic and extrinsic factors predicted lateral geniculate and medial mediodorsal volumes.InterpretationOur results might be reflective of the involvement of anterograde and retrograde degeneration from white matter demyelination and cerebrospinal fluid‐mediated damage in subregional thalamic volume loss.