Electroencephalogram (EEG) is characterized by high temporal resolution, and various EEG analysis methods have developed rapidly in recent years. The EEG microstate analysis method can be used to study the changes of the brain in the millisecond scale, and can also present the distribution of EEG signals in the topological level, thus reflecting the discontinuous and nonlinear characteristics of the whole brain. After more than 30 years of enrichment and improvement, EEG microstate analysis has penetrated into many research fields related to brain science. In this paper, the basic principles of EEG microstate analysis methods are summarized, and the changes of characteristic parameters of microstates, the relationship between microstates and brain functional networks as well as the main advances in the application of microstate feature extraction and classification in brain diseases and brain cognition are systematically described, hoping to provide some references for researchers in this field.