Abstract: Antibiotic abuse and environmental pollution caused by animal husbandry has aroused extensive concern from the government and the industry. As a kind of efficient alternative to agricultural chemicals like hormones and antibiotics, functional microorganisms can enhance the comprehensive growth performance of animals and thus play a crucial role in ecological and healthy breeding. The use of functional microorganisms in animal breeding for eco-agriculture has been a key development pathway for achieving the objective of sustainable development. Functional microorganisms are used at the beginning, middle, and end of the entire breeding process. Functional microorganisms can effectively eliminate anti-nutritional factors from feed sources, increasing their utilization rate and nutritional value. Animals fed with functional microorganisms not only have balanced gut microbiota and intestinal homeostasis, but their immune system is also well regulated. Functional microorganisms can also control odor emissions and pathogens in the environment. Finally, functional microorganisms also play an important role in the bio-safety treatment and circular utilization of breeding wastes. This study provides references for the continued application and promotion of functional microorganisms in animal breeding by summarizing the progress of their application and related mechanisms in such areas as feed processing, intestinal health, breeding environmental control and waste treatment.