During the past decade, mapping complex structural and functional networks in living human brain using non-invasive neuroimaging technologies has been widely developed and employed on a variety of cognitive and clinical neuroscience researches. Among all modern neuroimaging technologies, magnetic resonance imaging (MRI) has been considered as one of the most reliable and reproducible neuroimaging modalities for exploring the complex brain networks with adequate spatial and temporal resolutions. In this talk, I will introduce how we employ advanced MR neuroimaging techniques to map the brain connectivity and investigate the complex brain networks through graph theoretical analysis and computational algorithms. The applications on cognitive neuroscience and neurological diseases will also be introduced and discussed.