Reactive carbonyl compounds are a large group of highly reactive electrophilic compounds containing one or more carbonyl groups, which can be created by lipid oxidation both in vivo and in food. Malondialdehyde (MDA) and 4‐hydroxy‐2‐nonenel (HNE) are the two most important reactive carbonyl compounds in food. They can react with proteins and nucleic acids and cause biological damage to cells and lead to carbonyl stress. Therefore, they are regarded as representative products of lipid oxidation, toxic molecules, and biomarkers of oxidative stress. Apart from biological toxicity, they can also react with myoglobin and myofibrillar protein and further affect color, gel properties, hydrophobicity, or other properties of food. However, the effects of MDA and HNE on food qualities have not received as much attentions and it is noteworthy that the existing analytical methods for detecting MDA and HNE have a variety of limitations due to the complexity of food samples. To provide a comprehensive understanding of HNE and MDA, the formation mechanism, occurrence, and analytical methods for MDA and HNE in food matrix were summarized in this article. Emphasis is focused on formation mechanism including non‐enzymatic pathway and enzymatic pathway, and detection methods including the extraction methods, the new development of sample pre‐treatment technology and the selection of derivative reagents. Impressively, the reaction mechanism of MDA and HNE with myoglobin or myofibrillar protein is also described to explain how MDA and HNE affect food quality.