Some of the Aspergillus flavus have caused serious pollution to agricultural products. Affected by related genes, Aspergillus flavus will produce a mycotoxin, aflatoxin, which poses major health threats to humans and animals. Aflatoxin contamination may occur in the field, storage or transportation. There are many strategies to prevent aflatoxin from entering the food chain, among which the use of biological method, e.g. microorganisms to control aflatoxins pollution has attracted rising attention from researchers and has been gradually adopted by farmers. It has been widely reported that microorganisms and their metabolites can effectively reduce the pollution of Aspergillus flavus and aflatoxins to food crops and products. Functional components are mainly metabolites of microorganisms, including polypeptides, small molecular organic compounds, organic acids, antibiotics and enzymes. Because of the great economic impact of aflatoxin pollution on crops and its toxicological effects on humans and animals, this problem has attracted great attention all over the world. In this paper, the types of microorganisms, including Bacillus spp., Lactobacillus spp., yeast, Streptomyces spp. and some marine microorganisms, and related functional components that have antagonistic effects on Aspergillus flavus and aflatoxins were all reviewed. Moreover, the mechanism of inhibition on aflatoxins and the degradation of aflatoxins were also summarized, aiming to provide reference basis for biological control of Aspergillus flavus and aflatoxins pollution.