Aspergillus flavus is a ubiquitous pathogen that can infect many foods and grains, and it produces large amounts of aflatoxins during their storage. Aflatoxins are considered highly toxic and carcinogenic to humans, and they cause great damage to crop production, food security, and human health. Thus, controlling A. flavus and aflatoxins in grains presents a great challenge to humans worldwide. Over the past decade, many strategies have been demonstrated to be useful in controlling A. flavus and aflatoxins during food storage. These methods involve physical agents, chemical agents, biological agents, etc. Some of these methods are currently used in actual production. In this review, we summarize the reported methods for controlling A. flavus and aflatoxins during food storage in the past ten years and elucidate their advantages and disadvantages. The methods discussed include irradiation technology; low oxygen atmospheres; chemical fungicides (benzalkonium chloride, iodine, ammonium bicarbonate, and phenolic and azole compounds); biological agents from plants, animals, and micro-organisms; and aflatoxin elimination methods. We expect that this review will promote the applications of current strategies and be useful for the development of novel technologies to prevent or eliminate A. flavus and aflatoxins in food and feed during storage.