Fluorescence lifetime is not only associated with the molecular structure of fluorophores, but also strongly depends on the environment around them, which allows fluorescence lifetime imaging microscopy (FLIM) to be used as a tool for precise measurement of the cell or tissue microenvironment. This review introduces the basic principle of fluorescence lifetime imaging technology and its application in clinical medicine, including research and diagnosis of diseases in skin, brain, eyes, mouth, bone, blood vessels and cavity organs, and drug evaluation. As a noninvasive, nontoxic and nonionizing radiation technique, FLIM demonstrates excellent performance with high sensitivity and specificity, which allows to determine precise position of the lesion and, thus, has good potential for application in biomedical research and clinical diagnosis.