Food thermal processing is a crucial method for transforming raw materials into edible products suitable for long-term storage. However, while this process enhances the taste and extends the shelf life of food, it can also generate a range of chemical contaminants, including acrylamide, heterocyclic amines, furan, advanced glycation end-products, chloropropanols, polycyclic aromatic hydrocarbons and nitrosamines. These contaminants are believed to have carcinogenic, mutagenic and other toxic effects on human health. Metabolomics, as an emerging field of omics science, analyzes alterations in small molecules within cells and organisms to identify key metabolites and their associated pathways, thus providing valuable insights into the toxic mechanisms of food processing contaminants. This review first summarized the major contaminants produced during food thermal processing and their toxicological characteristics. It then discussed in detail the progress made in metabolomics in investigating the effects of these contaminants on the metabolic profiles of organisms and their associated toxic mechanisms. Additionally, the review addressed current challenges in metabolomics research, such as the complexity of metabolic products from food processing contaminants, difficulties in data analysis, and the lack of standardized experimental and analytical methods. Finally, the review highlights the future prospects of metabolomics in enhancing food safety assessments and identifying potential health risks, particularly through technological innovations and artificial intelligence to advance this field.