Structural covariance is described as coordinated variation in brain morphological features, such as cortical thickness and volume, among brain structures functionally or anatomically interconnected to one another. Structural covariance networks, based on graph theory, have been studied in mental disorders. This analysis can help in understanding the brain mechanisms of schizophrenia and bipolar disorder. We investigated cortical thickness-based individualized structural covariance networks in patients with schizophrenia and bipolar disorder. T1-weighted magnetic resonance images were obtained from 39 patients with schizophrenia, 37 patients with bipolar disorder type I, and 32 healthy controls, and cortical thickness was analyzed via a surface-based morphometry analysis. The structural covariance of cortical thickness was calculated at the individual level, and covariance networks were analyzed based on graph theoretical indices: strength, clustering coefficient (CC), path length (PL) and efficiency. At the global level, both patient groups showed decreased strength, CC and efficiency, and increased PL, compared to healthy controls. In bipolar disorder, we found intermediate network measures among the groups. At the nodal level, schizophrenia patients showed decreased CCs in the left suborbital sulcus and the right superior frontal sulcus, compared to bipolar disorder patients. In addition, patient groups showed decreased CCs in the right insular cortex and the left superior occipital gyrus. Global-level network indices, including strength, CCs and efficiency, positively correlated, while PL negatively correlated, with the positive symptoms of the Positive and Negative Syndrome Scale for patients with schizophrenia. The nodal-level CC of the right insular cortex positively correlated with the positive symptoms of schizophrenia, while that of the left superior occipital gyrus positively correlated with the Young Mania Rating Scale scores for bipolar disorder. Altered cortical structural networks were revealed in patients, and particularly, the prefrontal regions were more altered in schizophrenia. Furthermore, altered cortical structural networks in both patient groups correlated with core pathological symptoms, indicating that the insular cortex is more vulnerable in schizophrenia, and the superior occipital gyrus is more vulnerable in bipolar disorder. Our individualized structural covariance network indices might be promising biomarkers for the evaluation of patients with schizophrenia and bipolar disorder.