Schizophrenia (SZ) and autism spectrum disorder (ASD) sharing overlapping symptoms have a long history of diagnostic confusion. It is unclear what their differences at a brain level are. Here, we propose a multimodality fusion classification approach to investigate their divergence in brain function and structure. Using brain functional network connectivity (FNC) calculated from resting-state fMRI data and gray matter volume (GMV) estimated from sMRI data, we classify the two disorders using the main data (335 SZ and 380 ASD patients) via an unbiased 10-fold cross-validation pipeline, and also validate the classification generalization ability on an independent cohort (120 SZ and 349 ASD patients). The classification accuracy reached up to 83.08% for the testing data and 72.10% for the independent data, significantly better than the results from using the single-modality features. The discriminative FNCs that were automatically selected primarily involved the sub-cortical, default mode, and visual domains. Interestingly, all discriminative FNCs relating to the default mode network showed an intermediate strength in healthy controls (HCs) between SZ and ASD patients. Their GMV differences were mainly driven by the frontal gyrus, temporal gyrus, and insula. Regarding these regions, the mean GMV of HC fell intermediate between that of SZ and ASD, and ASD showed the highest GMV. The middle frontal gyrus was associated with both functional and structural differences. In summary, our work reveals the unique neuroimaging characteristics of SZ and ASD that can achieve high and generalizable classification accuracy, supporting their potential as disorder-specific neural substrates of the two entwined disorders.