Surface-enhanced Raman spectroscopy (SERS) is a rapid detection method with high sensitivity and simple pretreatment, but can be affected by interference from matrix components. By incorporating molecularly imprinted polymers (MIPs) that recognize specific targets, MIP-SERS sensors effectively overcome the interference of complex matrices and offer improved stability and sensitivity. This review provides a comprehensive understanding of the applications of MIP-SERS sensors for the detection of trace toxic substances in food. The underlying mechanism and development of SERS technology and the principle and classification of MIPs technology are discussed. Furthermore, the types of MIP-SERS sensors are introduced, with their advantages and disadvantages systematically illustrated. Recent advances in MIP-SERS technology for the detection of mycotoxins, additives, prohibited dyes, pesticides, veterinary drug residues, and other hazardous substances in food are highlighted. Finally, this review discusses the challenges associated with MIP-SERS technology and proposes future development prospects.