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Abstract Background Somatic Symptom Disorder (SSD) is a condition often linked to excessive health anxiety and somatic symptoms. In recent years, studies have found associations between the cerebellum and various mental illnesses, including SSD. However, the microstructure of cerebellar subregions in SSD using diffusion magnetic resonance imaging has not been fully defined. Methods This is a cross-sectional study, that included 30 SSD patients and 30 age- and gender-matched healthy controls to investigate the microstructure of the cerebellum using diffusion magnetic resonance imaging. SSD diagnosis followed DSM-5 criteria, excluding major psychiatric comorbidities, while healthy controls underwent rigorous screening to exclude psychiatric or neurological histories. Clinical evaluations utilized standardized scales to assess depressive, anxiety, and cognitive symptoms. MRI data were acquired using a 3T Siemens Prisma scanner, including T1-weighted and diffusion-weighted imaging (30 directions, b = 1000/2000 s/mm²). Multi-compartment diffusion magnetic resonance imaging metrics from free water elimination diffusion tensor imaging and neurite orientation dispersion and density imaging were used to observe microstructural changes in the cerebellum’s white matter and gray matter subregions in SSD patients. Results Compared to the control group, patients with SSD exhibited significant alterations in white matter microstructure. These changes were characterized by increased free water-eliminated fractional anisotropy and neurite density index, as well as decreased free water-eliminated mean diffusivity and radial diffusivity. Furthermore, the cerebellum displayed varying microstructural changes across 26 gray matter subregions. These changes included reduced mean diffusivity, free water-eliminated axial diffusivity, and free water-eliminated radial diffusivity, alongside increased neurite density index and orientation dispersion index. Importantly, the study identified significant correlations between these microstructural changes and clinical symptoms. Specifically, Vermis X and the left lobule VIIb showed significant associations with both depression and anxiety scores. Conclusions The findings suggest greater neurite density and enhanced diffusion restriction in the cerebellum of patients with SSD, which may indicate possible adaptive changes associated with chronic stress.