The invention provides a method and system for extracting abnormal parameters of the brain. The method comprises the following steps: carrying out magnetic resonance diffusion tensor imaging and resting-state functional imaging scanning for the brain, and obtaining diffusion tensor data and resting-state functional data of the brain; building the structural connection network of the brain according to the diffusion tensor data; building the functional connection network of the brain according to the resting-state functional data; coupling the structural connection network with the functional connection network to obtain network coupling indexes; arraying and verifying the network coupling indexes and normal network coupling indexes, and extracting the parameters which are different from the normal network coupling indexes in the network coupling indexes. The method and the system are used for conveniently extracting the parameters sensitively reflecting the abnormity of the structure and the function of the brain.