Livestock and poultry meat is one of the main consumption sources of fatty acids (FAs) in China. FAs are the main component of lipids and essential nutrients for the human body. The location of carbon–carbon double bond (CC) in unsaturated fatty acids (UFAs) significantly affects the nutrition and flavor quality of meat products. This study established an analytical method for identifying the CC positions of UFAs based on the Paternò-Büchi (PB) reaction using ultra-high performance liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF). The FA extract was derivatized with 2-acetylpyridine under ultraviolet light at 254 nm. The derivatized FA was then analyzed using targeted MS/MS mode in positive electrospray ionization. Limits of detection (LOD) and limits of quantitation (LOQ) of 21 UFAs were 0.004–0.680 and 0.013–2.267 μg/L, respectively. Furthermore, for the diagnostic ions at the same functional group terminal fragmented from derivatives of FA CC isomers, the abundance ratio was linear with that of the corresponding content, which could be applied to non-targeted screening of CC positions in FAs. Based on this method, a total of 28 UFAs were screened in five types of livestock and poultry meats in this study. Among them, four isomers of C17:1, four of C18:1, two of C18:2, two of C20:3 and two of C22:5 were identified. The precise identification and quantitation of the double bond positions of fatty acids will be of great significance for the exploration of the nutritional components in livestock and poultry meat.