Short-chain fatty acids (SCFAs), such as acetic acid, propionic acid, lactic acid, β-hydroxybutyric acid, and crotonic acid, play key biological roles and are also strongly associated with the maintenance of health and the development of age-related diseases. However, an accurate method for SCFA detection in human serum is lacking. Herein, we developed an UHPLC-QE-Orbitrap MS method based on 3nitrophenylhydrazine derivatization in negative electrospray ionization through parallel reaction monitoring mode for the simultaneous detection of 11 SCFAs in the serum, and the analysis was performed on an Agilent Proshell 120 EC-C 18 column (2.1 mm × 100 mm, 2.7 µm). Three pairs of isomers -isobutyric and butyric acid, isovaleric and valeric acid, and isocaproic and caproic acid-were completely separated in 20 min in a single run. Our method exhibited satisfactory linearity (r > 0.99) for all analytes, and both intrabatch and interbatch accuracies (73.74-127.9%) and precisions ( 21%) were acceptable. The extraction recoveries of all analytes were 90.80-111.7%, and the IS-normalized matrix effects were 74.43-116.9%. This optimized method was successfully applied to a cohort of 1021 older Chinese individuals. Our results may further the understanding of the metabolic phenotypes associated with SCFAs in other populations.