A system for predicting disease with graph convolutional neural network based on multimodal magnetic resonance imaging, which extracts the radiomics information of multiple brain regions across modals as the features of nodes from multimodal magnetic resonance data, and extracts the connectomics information between brain regions to form an adjacency matrix. T1-weighted structural images extract cortical information through cortical reconstruction, and resting-state magnetic resonance data are used to calculate amplitude of low frequency fluctuations, regional homogeneity and functional connectivity. Through multimodal data preprocessing, image index extraction and structured data integration, multimodal unstructured magnetic resonance image data are integrated into unified graph-structured data, and the disease is predicted by a graph convolutional neural network method. The system can better integrate the cross-modal physiological indexes of multiple brain regions and the correlation between brain regions and improve prediction ability of the model and generalization ability of the model with different diseases.