The human gut microbiota is a metabolic organ that plays an essential role in human health and disease. The molecular mechanisms of its involvement in processes such as host food digestion, immunity and brain function are the synergistic coupling of specific metabolic pathways between microorganism and human. Enzymes are the basic functional units that involved in the transformation of substances in the metabolic pathways. An in-depth look into the catalytic mechanisms of the enzymes encoded by human gut microbiota will provide a theoretical framework for exploring the interventions of precision nutrition and medicine targeting the human gut microbiota (or intestinal enzymes). Studies on enzymatic hydrolysis of specific substrates have shown that the human gut microbiota not only encodes all known families of carbohydrate active enzymes (CAZYmes), but also contains plenty of the potentially novel CAZYmes. This paper describes the principles of classification and catalytic properties of CAZYmes, and mainly reviews the research progresses on the crystal structures of novel CAZYmes derived from the human gut microbiota.