The emergence of several chemical substances continues to enrich and facilitate the development of food science, but their irrational use also poses a threat to food safety and human health. Nontargeted screening (NTS) has become an important tool for rapid traceability and efficient identification of chemical hazards in food matrices. NTS in food analysis is highly integrated with sample pretreatment, instrumental analysis platforms, data acquisition and analysis, and toxicology. This article is a systemic review of current sample preparation, analytical platforms, and toxicity-guided NTS techniques and provides the latest advancements in workflows and innovative applications of the NTS process based on mass spectrometric techniques. High-throughput toxicity screening platforms play an important role in NTS of unknown chemical hazards of complex food matrices. Advanced machine learning and artificial intelligence are increasingly accessible fields that may effectively process large-scale screening data and advance food NTS research.