Schizophrenia (SZ) and autism spectrum disorder (ASD) share considerable clinical features and intertwined historical roots. It is greatly needed to explore their similarities and differences in pathophysiologic mechanisms. We assembled a large sample size of neuroimaging data (about 600 SZ patients, 1000 ASD patients, and 1700 healthy controls) to study the shared and unique brain abnormality of the two illnesses. We analyzed multi-scale brain functional connectivity among functional networks and brain regions, intra-network connectivity, and cerebral gray matter density and volume. Both SZ and ASD showed lower functional integration within default mode and sensorimotor domains, but increased interaction between cognitive control and default mode domains. The shared abnormalties in intra-network connectivity involved default mode, sensorimotor, and cognitive control networks. Reduced gray matter volume and density in the occipital gyrus and cerebellum were observed in both illnesses. Interestingly, ASD had overall weaker changes than SZ in the shared abnormalities. Interaction between visual and cognitive regions showed disorder-unique deficits. In summary, we provide strong neuroimaging evidence of the convergent and divergent changes in SZ and ASD that correlated with clinical features.