The invention relates to a brain link mining system and method based on document analysis and functional nuclear magnetic resonance imaging analysis, and belongs to the fields of computer technologies and cognitive neuroscience technologies. The system comprises a dynamic causal model module, an activation analysis module, a document link analysis module, a seeking sub-network module, a document database and a brain network link database. The method comprises the steps of firstly, by calculating the activated probabilities of all brain coordinates in all documents, figuring out the activated probabilities of corresponding anatomical areas to obtain activated brain areas, mining modes which frequently appear in the brain areas through the association rules algorithm, calculating confidence coefficients to obtain a trusted brain function network, establishing the corresponding documents to generate a brain network database, then collecting corresponding functional nuclear magnetic resonance imaging data by utilizing a functional nuclear magnetic resonance imaging system, and verifying the actual link direction and weight numbers of a network edge by utilizing the dynamic causal model module. In this way, the problem that calculating is overlong in time and low in accuracy in the brain link analysis process is solved.