With the advance in science and technology as well as the improvement of living standards, the function of food is no longer just to meet the needs of survival. Food science and its associated nutritional health issues have been increasingly debated. Lipids, as complex metabolites, play a key role both in food and human health. Taking advantages of mass spectrometry (MS) by combining its high sensitivity and accuracy with extensive selective determination of all lipid classes, MS‐based lipidomics has been employed to resolve the conundrum of addressing both qualitative and quantitative aspects of high‐abundance and low‐abundance lipids in complex food matrices. In this review, we systematically summarize current applications of MS‐based lipidomics in food field. First, common MS‐based lipidomics procedures are described. Second, the applications of MS‐based lipidomics in food science, including lipid composition characterization, adulteration, traceability, and other issues, are discussed. Third, the application of MS‐based lipidomics for nutritional health covering the influence of food on health and disease is introduced. Finally, future research trends and challenges are proposed. MS‐based lipidomics plays an important role in the field of food science, promoting continuous development of food science and integration of food knowledge with other disciplines. New methods of MS‐based lipidomics have been developed to improve accuracy and sensitivity of lipid analysis in food samples. These developments offer the possibility to fully characterize lipids in food samples, identify novel functional lipids, and better understand the role of food in promoting healt.