Food safety is a worldwide concern and is directly related to human health. Therefore, convenient, effective, and economical methods and technologies for food safety analysis have been developed continuously. Magnetic molecularly imprinted polymers (MMIPs) have gained extensive attention in recent years, as they have high selectivity, high adsorption capacity, and are easy to isolate from food samples. Recently, advanced strategies for the synthesis of MMIPs have been proposed to solve problems of template leakage and non-specific adsorption, and to increase the biocompatibility, adsorption rate, as well as adsorption capacity of the imprinted materials. In this review, we focus on new attempts at modification of magnetic core and MMIPs’ surfaces, and the selection of template, functional monomer, cross-linker as well as porogen. Studies are summarized that used advanced MMIPs for the recognition and adsorption of pesticide residues, veterinary drug residues, mycotoxins, contaminants, and adulterations in foodstuffs over the last 5 years. Finally, some still existing challenges and future prospects to further promote MMIPs properties are also discussed.