Progresses in studies of complex networks and its applications in brain network were retrospected,including the research on topology structure features of anatomical and functional brain networks,as well as on the relationship between brain structures and functions.Based on complex networks theory,some important topology features of anatomical and functional brain networks were reported,such as small world,scale free,modular and hub regions;then some new findings were presented about the relationship between cognitive function and neuropsychiatry disorder with abnormalities in functional connectivity and changes in topological structure changes.Several challenges and key issues that should be addressed in the future were further raised.