Major depressive disorder (MDD) is a neuropsychiatric condition with high lifetime prevalence and suicide attempt rate. Developing useful biomarkers with diagnostic and prognostic value is of great importance for a better understanding of the pathophysiology as well as the treatment guidance of MDD. This lecture will briefly review the progresses in MR-based structural (MRI, Diffusion MRI), functional (BOLD-fMRI, ASL-fMRI), and metabolic imaging (MRS, MRSI) of the brain, which have provided significant insights into the pathophysiology of MDD in clinical settings.