Abstract: Emerging mycotoxins are mycotoxins that have emerged in recent years, encompassing more than ten different families of mycotoxins, primarily Alternaria toxins (ATs), enniatins (ENNs), and beauvericin (BEA). These contaminants are widely found in a variety of food groups including cereals, fruits and vegetables, beer, wine, beans, and potatoes. Studies have shown that multiple physiological toxicities of the emerging mycotoxins are identified in plants, animals, and various human cell lines, and their presence are associated with certain human diseases. Notably, the emerging mycotoxins are not only prevalent in food but also frequently detected in human biological samples (e.g., serum, urine, and breast milk). Furthermore, multiple risk assessment studies have indicated that dietary exposure to the emerging mycotoxins, particularly ATs, exceed safe levels in some populations, posing potential threats to both food safety and human health. This article reviewed the contamination and physiological toxicity of three major emerging mycotoxins—ATs, ENNs, and BEA—in food, as well as research progress in human exposure assessment by different risk evaluation methods (e.g., dietary contamination & intake assessment and human biomonitoring). Additionally, it discussed current research challenges and unresolved scientific issues, aiming to provide insights for the biological control of emerging mycotoxins in food and the assessment of their exposure risks in human populations.