This review (with 126 references) aims at providing an updated overview of the recent developments and innovations of the preparation and application of magnetic nanoparticles for food safety analysis. During the past two decades, various magnetic nanoparticles with different sizes, shapes, and surface modifications have been designed, synthesized, and characterized with the prospering development of material science. Analytical scientists and food scientists are among the ones who bring these novel materials from laboratories to commercial applications. Powerful and versatile surface functional groups and high surface to mass ratios make these magnetic nanoparticles useful tools for high-efficiency capture and preconcentration of certain molecules, even when they exist in trace levels or complicated food matrices. This is why more and more methods for sensitive detection and quantification of hazards in foods are developed based on these magic magnetic tools. In this review, the principles and superiorities of using magnetic nanoparticles for food pollutant analysis are first introduced, like the mechanism of magnetic solid phase extraction, a most commonly used method for food safety-related sample pretreatment. Their design and preparation are presented afterward, alongside the mechanisms underlying their application for different analytical purposes. After that, recently developed magnetic nanoparticle-based methods for dealing with food pollutants such as organic pollutants, heavy metals, and pathogens in different food matrices are summarized in detail. In the end, some humble outlooks on future directions for work in this field are provided.