Kefir is a mildly alcoholic dairy beverage made from cow’s, goat’s or sheep’s milk fermented with kefir grains, which mainly consist of lactic acid bacteria, acetic acid bacteria and yeast. Due to its unique flavor and taste, as well as outstanding probiotic effects, kefir is increasingly attracting attention from consumers. As a natural starter culture, kefir grains have a complex structure and rich microbial composition. At present, fermentation with a starter culture consisting of microbial strains isolated from kefir grains is mainly used for the industrial production of kefir. This article reviews the microbial composition of kefir grains, the impact of kefir grains from different regions and raw materials on microbial diversity during the kefir fermentation process, and summarizes the current progress in research on flavor substances in kefir.