As a novel non-thermal sterilization technology, the magnetic field has attracted much attention due to its strong penetrability and green and safe characteristics. Oscillating magnetic fields can effectively eliminate microorganisms and prolong the shelf life of food while maintaining the nutritional properties of food, and static magnetic fields have also shown great potential in inhibiting the growth of microorganisms in food. However, the mechanisms of inhibition and inactivation of microorganisms in food by different types of magnetic fields have not been systematically elaborated and analyzed. Therefore, this paper reviews the research progress of magnetic fields in eliminating and inhibiting microorganisms in food, encompassing the perspectives of mechanisms of action and application scenarios, and discusses the prospects and challenges faced by this technology.