Systemic lupus erythematosus is a complex autoimmune disease known for its diverse clinical manifestations, including neuropsychiatric systemic lupus erythematosus, which impacts a patient's quality of life. Our aim was to explore the relationships among brain MR imaging morphometric findings, neuropsychiatric events, and laboratory values in patients with systemic lupus erythematosus, shedding light on potential volumetric biomarkers and diagnostic indicators for neuropsychiatric systemic lupus erythematosus. Twenty-seven patients with systemic lupus erythematosus (14 with neuropsychiatric systemic lupus erythematosus, 13 with systemic lupus erythematosus), 24 women and 3 men (average age, 43 years, ranging from 21 to 62 years) were included in this cross-sectional study, along with 10 neuropsychiatric patients as controls. An MR imaging morphometric analysis, with the VolBrain online platform, to quantitatively assess brain structural features and their differences between patients with neuropsychiatric systemic lupus erythematosus and systemic lupus erythematosus, was performed. Correlations and differences between MR imaging morphometric findings and laboratory values, including disease activity scores, such as the Systemic Lupus Erythematosus Disease Activity Index and the Systemic Lupus International Collaborating Clinics Damage Index, were explored. An ordinary least squares regression analysis further explored the Systemic Lupus Erythematosus Disease Activity Index and Systemic Lupus International Collaborating Clinics Damage Index relationship with MR imaging features. For neuropsychiatric systemic lupus erythematosus and non-neuropsychiatric systemic lupus erythematosus, the brain regions with the largest difference in volumetric measurements were the insular central operculum volume (P value = .003) and the occipital cortex thickness (P = .003), which were lower in neuropsychiatric systemic lupus erythematosus. The partial correlation analysis showed that the most correlated morphometric features with neuropsychiatric systemic lupus erythematosus were subcallosal area thickness asymmetry (P < .001) and temporal pole thickness asymmetry (P = .011). The ordinary least squares regression analysis yielded an R 2 of 0.725 for the Systemic Lupus Erythematosus Disease Activity Index score, with calcarine cortex volume as a significant predictor, and an R 2 of 0.715 for the Systemic Lupus International Collaborating Clinics Damage Index score, with medial postcentral gyrus volume as a significant predictor. The MR imaging volumetric analysis, along with the correlation study and the ordinary least squares regression analysis, revealed significant differences in brain regions and their characteristics between patients with neuropsychiatric systemic lupus erythematosus and those with systemic lupus erythematosus, as well as between patients with different Systemic Lupus Erythematosus Disease Activity Index and Systemic Lupus International Collaborating Clinics Damage Index scores.