Children with autism spectrum disorders (ASD) often exhibit motor clumsiness (Developmental Coordination Disorder, DCD), i.e. they struggle with everyday tasks that require motor coordination like dressing, self‐care, and participating in sport and leisure activities. Previous studies in these neurodevelopmental disorders have demonstrated functional abnormalities and alterations of white matter microstructural integrity in specific brain regions. These findings suggest that the global organization of brain networks is affected in DCD and ASD and support the hypothesis of a ‘dys‐connectivity syndrome’ from a network perspective. No studies have compared the structural covariance networks between ASD and DCD in order to look for the signature of DCD independent of comorbid autism. Here, we aimed to address the question of whether abnormal connectivity in DCD overlaps that seen in autism or comorbid DCD‐autism. Using graph theoretical analysis, we investigated differences in global and regional topological properties of structural brain networks in 53 children: 8 ASD children with DCD (DCD+ASD), 15 ASD children without DCD (ASD), 11 with DCD only, and 19 typically developing (TD) children. We constructed separate structural correlation networks based on cortical thickness derived from Freesurfer. The children were assessed on the Movement‐ABC and the Beery Test of Visual Motor Integration. Behavioral results demonstrated that the DCD group and DCD+ASD group scored on average poorer than the TD and ASD groups on various motor measures. Furthermore, although the brain networks of all groups exhibited small‐world properties, the topological architecture of the networks was significantly altered in children with ASD compared with DCD and TD. ASD children showed increased normalized path length and higher values of clustering coefficient. Also, paralimbic regions exhibited nodal clustering coefficient alterations in singular disorders. These changes were disorder‐specific, and included alterations in clustering coefficient in the isthmus of the right cingulate gyrus and the pars orbitalis of the right inferior frontal gyrus in ASD children, and DCD‐related increases in the lateral orbitofrontal cortex. Children meeting criteria for both DCD and ASD exhibited topological changes that were more widespread from those seen in children with only DCD, i.e. children with DCD+ASD showed alterations of clustering coefficient in (para)limbic regions, primary areas, and association areas. The DCD+ASD group showed changes in clustering coefficient in the left association cortex relative to the ASD group. Finally, the DCD+ASD group shared ASD‐specific abnormalities in the pars orbitalis of right inferior frontal gyrus, which was hypothesized to reflect atypical emotional‐cognitive processing. Our results provide evidence that DCD and ASD are neurodevelopmental disorders with a low degree of overlap in abnormalities in connectivity. The co‐occurrence of DCD+ASD was also associated with a distinct topological pattern, highlighting the unique neural signature of comorbid neurodevelopmental disorders. Children with Autism Spectrum Disorders (ASD) and Developmental Coordination Disorder (DCD) were simultaneously investigated with graph theoretical analyses. The co‐occurrence of DCD+ASD was associated with a distinct topological pattern. These results will aid in providing better definitions for comorbid neurodevelopmental disorders.