Background and ObjectiveSpinal muscular atrophy (SMA) is one of the most common monogenic neuromuscular diseases, and the pathogenesis mechanisms, especially the brain network topological properties, remain unknown. This study aimed to use individual‐level morphological brain network analysis to explore the brain neural network mechanisms in SMA.MethodsIndividual‐level gray matter (GM) networks were constructed by estimating the interregional similarity of GM volume distribution using both Kullback–Leibler divergence‐based similarity (KLDs) and Jesen‐Shannon divergence‐based similarity (JSDs) measurements based on Automated Anatomical Labeling 116 and Hammersmith 83 atlases for 38 individuals with SMA types 2 and 3 and 38 age‐ and sex‐matched healthy controls (HCs). The topological properties were analyzed by the graph theory approach and compared between groups by a nonparametric permutation test. Additionally, correlation analysis was used to assess the associations between altered topological metrics and clinical characteristics.ResultsCompared with HCs, although global network topology remained preserved in individuals with SMA, brain regions with altered nodal properties mainly involved the right olfactory gyrus, right insula, bilateral parahippocampal gyrus, right amygdala, right thalamus, left superior temporal gyrus, left cerebellar lobule IV–V, bilateral cerebellar lobule VI, right cerebellar lobule VII, and vermis VII and IX. Further correlation analysis showed that the nodal degree of the right cerebellar lobule VII was positively correlated with the disease duration, and the right amygdala was negatively correlated with the Hammersmith Functional Motor Scale Expanded (HFMSE) scores.ConclusionsOur findings demonstrated that topological reorganization may prioritize global properties over nodal properties, and disrupted topological properties in the cortical–limbic‐cerebellum circuit in SMA may help to further understand the network pathogenesis underlying SMA.