Foods, agricultural by-products and medicinal plants are often contaminated by pathogenic fungi and mycotoxins. Pathogenic fungi not only lead to food deterioration, but also harm people’s health. The commonly used methods for detoxification include physical, chemical and biological methods. A large number of studies have shown that natural plant essential oils inhibit the growth of pathogenic fungi and the accumulation of mycotoxins and have good biodegradability, making them a promising environmental-friendly alternative to traditional synthetic fungicides. In this review, the classification and harm of common pathogenic fungi and mycotoxins, as well as the antifungal components and mechanisms of plant essential oils are introduced, and recent progress on plant essential oils in the control of pathogenic fungi and mycotoxins is summarized. This review provides a theoretical basis for the development and application of plant essential oils.