Neurological and psychiatric disorders disturb higher cognitive functions and are accompanied by aberrant cortico-cortical axonal pathways or synchronizations of neural activity. A large proportion of neuroimaging studies have focused on examining the focal morphological abnormalities of various gray and white matter structures or the functional activities of brain areas during goal-directed tasks or the resting state, which provides vast quantities of information on both the structural and functional alterations in the patients' brain. However, these studies often ignore the interactions among multiple brain regions that constitute complex brain networks underlying higher cognitive function. Information derived from recent advances of noninvasive magnetic resonance imaging (MRI) techniques and computational methodologies such as graph theory have allowed researchers to explore the patterns of structural and functional connectivity of healthy and diseased brains in vivo. In this article, we summarize the recent advances made in the studies of both structural (gray matter morphology and white matter fibers) and functional (synchronized neural activity) brain networks based on human MRI data pertaining to neuropsychiatric disorders. These studies bring a systems-level perspective to the alterations of the topological organization of complex brain networks and the underlying pathophysiological mechanisms. Specifically, noninvasive imaging of structural and functional brain networks and follow-up graph-theoretical analyses demonstrate the potential to establish systems-level biomarkers for clinical diagnosis, progression monitoring, and treatment effects evaluation for neuropsychiatric disorders.