This study investigated the topological structural characteristics of systemic lupus erythematosus (SLE) with and without neuropsychiatric symptoms (NPSLE and non-NPSLE), and explore their clinical implications.We prospectively recruited 50 patients with SLE (21 non-NPSLE and 29 NPSLE) and 32 age-matched healthy controls (HCs), using MRI diffusion tensor imaging. Individual structural networks were constructed using fibre numbers between brain areas as edge weights. Global metrics (eg, small-worldness, global efficiency) and local network properties (eg, degree centrality, nodal efficiency) were computed. Group comparisons of network characteristics were conducted. Clinical correlations were assessed using partial correlation, and differentiation between non-NPSLE and NPSLE was performed using support vector classification.Patients with oth non-NPSLE and NPSLE exhibited significant global and local topological alterations compared with HCs. These changes were more pronounced in NPSLE, particularly affecting the default mode and sensorimotor networks. Topological changes in patients with SLE correlated with lesion burdens and clinical parameters such as disease duration and the systemic lupus international collaborating clinics damage index. The identified topological features enabled accurate differentiation between non-NPSLE and NPSLE with 87% accuracy.Structural networks in patients SLE may be altered at both global and local levels, with more pronounced changes observed in NPSLE, notably affecting the default mode and sensorimotor networks. These alterations show promise as biomarkers for clinical diagnosis.© Author(s) (or their employer(s)) 2024. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.