As resident immune cells of the central nervous system, microglia play critical roles in immune surveillance, immune responses, as well as in the development and maintenance of the nervous system. Microglia exhibit a high degree of heterogeneity and sensitivity, and research into their complex regulatory mechanisms and diverse functions has become a major focus in brain science. This article provides a comprehensive overview of methods for studying microglial morphology and function based on traditional research models and high-throughput sequencing technologies. It covers in vivo and in vitro models, microscopic imaging and visualization techniques, as well as analysis methods based on sequencing data. The characteristics and application scopes of these approaches are summarized, providing references for future multidimensional investigations into microglial phenotypic changes and functions.