BackgroundEarly-onset schizophrenia (EOS) and autism spectrum disorder (ASD) are two mental disorders with abnormal neurodevelopment and overlapping clinical symptoms. However, few prospective multi-center imaging studies explored their pathophysiological differences and similarities comprehensively. MethodsWe utilized a large cohort of functional magnetic resonance imaging data with standardized scanning protocols from 594 participants (276 participants with high-functioning ASD, 187 participants with EOS, and 131 normal controls (NCs)) recruited at five centers. A comprehensive evaluation of anatomical and connectomic features, including cortical thickness, subcortical nuclei volume, functional connectivity, functional gradients, and network efficiency, was conducted, culminating in the construction of imaging-based neuro-profiles for individuals with EOS and ASD. ResultsThe derived neuro-profiles revealed that EOS is characterized by more pronounced reductions in cortical thickness and subcortical nuclei volumes. In contrast, ASD exhibited more pronounced abnormalities in connectomic attributes. The decreased network functional connectivity and compressed functional gradients in ASD are likely to contribute to reduced network efficiency. Classifiers based on imaging profiles successfully distinguished individuals with EOS, ASD, and NCs with commendable performance in leave-site-out cross-validation (area under the operating characteristic curve (AUC) for ASD vs. NC: 0.769, AUC for ASD vs. EOS: 0.792, AUC for EOS vs. NC: 0.854). ConclusionThe neuro-profiles revealed that EOS and ASD exhibit overlapping as well as unique imaging characteristics; however, EOS exhibits greater structural variation, while ASD presents with more subtle connectomic abnormalities. These findings offer valuable insights into the distinct neurobiological mechanisms of EOS and ASD and enhance the prospect of early diagnosis through objective imaging-based biomarkers.