The physiological and pathological organs and tissues in human body can be observed by magnetic resonance imaging(MRI),which regarded as a fundamental complement for traditional cognition methods of human body by governing exterior to infer interior in traditional Chinese medicine(TCM).In recent years,the research of syndrome differentiation and classification based on MRI have found that,diseases such as lumbar disc herniation,knee osteoarthritis,cervical spondylosis,osteonecrosis of femeral head,breast cancer,mastitis and stroke,there are differences on the local morphological structure changes among various patterns,especially,there are significant differences between syndrome of excess and deficiency. Combined with MRI application,the morphological structure changes in body caused by compound of Chinese medicine could be observed more intuitively,acupuncture on dangerous acupoints could be tested in vivo owing to the avoidance of important organs injury. The application of functional magnetic resonance imaging (fMRI) has found that acupuncture on acupoints in different meridians could show superposed activation on the same brain region. fMRI is possible to more widely observe the functional changes of various tissue structures,which may be the research direction of TCM syndrome differentiation and efficacy judgement in the future.