Major Depression Disorder(MDD) is a complex mental disorder that characterized by various symptoms including motor, vegetative, cognitive, and affective abnormalities. It is one of the world’s leading causes of disability, lifetime prevalence estimates vary from 8% to 12%. MDD is moderately heritable, identification of genes that underlie susceptibility to MDD would be a major advance in our understanding of its pathophysiological mechanisms, and lead to improved prevention and the development of new and more effective therapies. Although hundreds of behavioral and pharmacogenetic association studies had been performed, clinical association studies still suffer from a lack of replication. Effects of single genes that have been linked to MDD have proven to be much smaller than originally expected and their pathogenetic influence is far more complicated by gene–gene interactions, gene–environment interactions and disease heterogeneity. In order to address these issues, many have advocated for the use of intermediate phenotype approach. Intermediate phenotypes describe neurobiological or neuropsychological traits that are linked to both genetic heritability and clinical disorder, they are presumably not only more specific, quantifiable, and reliable than diagnostic phenotypes, but also more proximal to gene function. Neural intermediate phenotypes measured by modern neuroimaging techniques are thought to more directly index the underlying neurobiology of complex phenotypes and hence have the intrinsic potential to bridge the gap between genes and psychiatric diagnostic phenotypes. The rapidly growing field of imaging genetics utilizing neuroimaging as tool to detect the subtle neural impact of genetic variants. More and more researchers used imaging genetic approach to investigate how depression-related genetic polymorphisms influence neural activity. Recent research showed that variants of genes involve in serotoninergic function (i.e.5-HTTLPR, HTR1A, MAOA, TPH2) associated with alterations of emotion-related neural activity or structure in the amygdala, anterior cingulate cortex, hippocampus, hypothalamus and functional connectivity between them. These regions are thought to be core regions in the pathophysiology of MDD. Other variants of genes that controlling biochemical like dopamine, CRH, BDNF, NPY, FKBP5 impacted the function of brain regions that underlie the reward processing and stress response. Research also found that most of these genes interact with life stressors, suggested that gene-environment interactions played an important role in the pathogenesis of MDD. Future studies should focus on the following aspects: (1)To address the complex nature of human genome, researchers should move beyond candidate gene studies, using genome-wide approach to overcome the selection bias. (2)At the neural level, future imaging genetics studies in MDD may want to combine biochemical measures (e.g. PET and MRS) with fMRI and genetic measures, and integrate structural and functional imaging data. (3)Researchers should attach great importance to the measurement of environmental factors, use observational measures and multiple well-validated measures to make the measurements more reliable. Moreover, future researchers may want to investigate G×E interaction under the framework of “differential susceptibility model”. (4)To further understand the causes and development of MDD, future studies should integrate neuroimaging, genetic, personality and social environmental factors, using longitudinal study paradigm to construct a comprehensive model of MDD.