A massive variety of microorganisms live in and on the human body, especially at oral, skin, vaginal, gastrointestinal, and respiratory sites. The complicated metabolic activities of microorganisms assist human digestive function and participate in a series of physiological and pathogenetic processes. Carbohydrate-active enzymes (CAZymes) are a series of enzymes that function in degradation, modification, and formation of glycoside bonds. Microbes regulate the physiological and pathogenetic processes of human body by producing various CAZymes to degrade and modify complex carbohydrates and generate signal molecules for further utilization in human cells. Here, we reviewed the mechanisms of complex carbohydrate metabolism and related microbial CAZymes, especially in digestive tract and oral cavity. We also summarized the relationship between microbial CAZymes and human health, and proposed potential applications.