Indole, also known as 2,3-benzopyrrole, is a typical nitrogen heterocyclic pollutant compound that is widely used in the chemical, pharmaceutical, dye and other industries. Meanwhile, it is a representative microbial metabolite in natural habitats and can be synthesized, transformed and degraded all the time. Besides, indole has a significant effect on various biological functions, such as the formation of microbial biofilms, motility, toxicity, plasmid stability, and even antibiotic resistance of the microbes. Thus, indole has been considered as a new and multifunctional inter-specific and inter-kingdom signaling molecule, playing an important role in bacterial physiology and animal behavior. Therefore, studying the mechanism of indole metabolism mediated by microorganisms as well as elucidating the basis of biological functions might be the key to reveal its fate and ecological significance to natural environment. In this review, the microbial resources and pathways of indole metabolism are systematically summarized. The important functions as signal molecules are also introduced, and the interactions of indoles-microorganisms are illustrated. The review provides important theoretical reference for revealing the metabolic mechanism of indole in complex environments.