Aspergillus species are ubiquitous fungi that produce mycotoxins (secondary metabolites) known as sterigmatocystin and aflatoxins in many different kinds of foods, which leads to serious contamination in agricultural products, thereby endangering human health. Extensive studies on Aspergillus fungi have been conducted on growth and development, aflatoxin biosynthesis, and their interactions with environment. Here, we summarized a series of functional genes of the main Aspergillus fungi relative to toxins occurrence in foods, which revealed the signal transduction mechanisms of their involvement in growth and development, toxin production, and response to light, anticipating providing theoretical guidance on developing control and prevention technologies for mycotoxin contamination in agricultural products to ensure food safety.