With the exacerbation of aging population in China, the number of patients with Alzheimer's disease (AD) is increasing rapidly. AD is a chronic but irreversible neurodegenerative disease, which cannot be cured radically at present. In recent years, in order to intervene in the course of AD in advance, many researchers have explored how to detect AD as early as possible, which may be helpful for effective treatment of AD. Imaging genomics is a kind of diagnosis method developed in recent years, which combines the medical imaging and high-throughput genetic omics together. It studies changes in cognitive function in patients with AD by extracting effective information from high-throughput medical imaging data and genomic data, providing effective guidance for early detection and treatment of AD patients. In this paper, the association analysis of magnetic resonance image (MRI) with genetic variation are summarized, as well as the research progress on AD with this method. According to complexity, the objects in the association analysis are classified as candidate brain phenotype, candidate genetic variation, genome-wide genetic variation and whole brain voxel. Then we briefly describe the specific methods corresponding to phenotypic of the brain and genetic variation respectively. Finally, some unsolved problems such as phenotype selection and limited polymorphism of candidate genes are put forward.