The food infected by Alternaria species can produce Alternaria toxins with genotoxicity, cytotoxicity, reproductive toxicity, and developmental toxicity. Due to the low content of Alternaria toxins with greatly different chemical structures in food, it is necessary to establish a reliable and highly sensitive method for Alternaria toxins residues analysis in food. Sample pretreatment is not only an important part but also a bottleneck in the process of residue analysis. This article reviewed the sample pretreatment technology of Alternaria toxins in food, specifically focusing on the application of QuEChERs, dispersed liquid-liquid microextraction, molecular imprinting solid phase extraction, and direct dilution method in Alternaria toxins extraction, as well as the applications of solid-phase extraction, dispersed solid-phase extraction, low- temperature freezing, and liquid-liquid distribution in the purification process of Alternaria toxins in food matrices. The advantages and disadvantages of different extraction and purification technologies were summarized. The advantages and limitations of existing pre-treatment technologies were analyzed. The development prospects of pre-treatment technologies were discussed, such as preparing new molecularly imprinted solid-phase extraction materials and purification materials with good performance and establishing an integrated detection system for extracting and analyzing Alternaria toxins in food.