Abstract: Free fatty acids and bile acids are two types of endogenous small molecule metabolites with carboxylic acid groups. They have diverse structures and abundant varieties, and play important physiological roles in regulating the body's metabolism and maintaining basic life activities. Studies have shown that metabolic disorders of free fatty acids and bile acids are closely related to the occurrence and development of non-alcoholic fatty liver disease, inflammatory bowel disease, cardiovascular and cerebrovascular diseases, diabetes and other diseases. The realization of high-sensitivity and broad-coverage quantitative analysis is crucial for early diagnosis, mechanism research, and drug target discovery in related diseases. This article summarizes the structural characteristics and classification of free fatty acids and bile acids, and reviews the research progress in their analytical methods.