Every year, more than 20,000,000 patients were plagued by brain diseases worldwide. Brain diseases include stroke, brain tumors, alzheimer's disease,parkinson's disease and many other diseases. Common diagnostic methods include computed tomography (CT), magnetic resonance imaging (MRI), positron emission tomography, etc, and among these methods, MRI is the diagnostic method with the best safety, the highest detection rate and the best reproducibility. As an advanced imaging technique, MRI has the advantages of non-invasive, non-radioactive, multi-parameter imaging, which means MRI has an indelible role in diagnosing brain diseases. MRI can be divided into perfusion weighted imaging (PWI), diffusion weighted imaging (DWI) and functional magnetic resonance imaging (fMRI). This paper focuses on the technical principles, characteristics and clinical applications of these three methods, for the purpose of promoting the development of magnetic resonance technology and the advancement of clinical diagnosis and treatment of brain diseases.