Altered cerebral structure and function have been observed in young survivors of acute lymphoblastic leukemia (ALL). However, the topological organization of the morphological brain networks (MBNs) has not yet been investigated at the individual level. Twenty-three young survivors of ALL and twenty healthy controls (HCs) were recruited and underwent T1-weighted magnetic resonance imaging (MRI) scanning. After preprocessing and segmentation, individual-based MBNs were constructed based on the morphological similarity of gray matter using the combined Euclidean distance. Young survivors showed a significantly lower global clustering coefficient (p = 0.008) and local efficiency (p = 0.035) compared with HCs. In addition, ALL survivors exhibited bidirectional alterations (decreases and increases) in nodal centrality and efficiency around the Rolandic operculum and posterior occipital lobe (p < 0.05, false discovery rate (FDR) corrected). Altered nodal topological efficiencies were associated with off-therapy duration and verbal memory capacity in the digit span test (p < 0.05, FDR corrected). Network-based statistical analysis revealed decreased morphological connections mainly in the pallidum subnetwork, which was negatively correlated with off-therapy durations (p < 0.05). Overall, the topological organization of the individual-based MBNs was disrupted in the young survivors of ALL, which may play a crucial role in executive efficiency deficits.