Abstract: N-methyl-N-(trimethylsilane) trifluoroacetamide (MSTFA) is an important derivatization reagent, the attribution of its mass spectrum peak is of great significance for the further study of its reaction mechanism. Therefore, density functional theory (DFT) is used for the first time in this work, at the B3LYP/6-311G** level, the mechanism of mass spectrometry cracking reaction of MSTFA and its fluorine-containing derivatives and the competition of cracking reaction were studied. Through the structural optimization, vibration analysis and layout analysis of each stationary point, as well as the calculation of bonding process and energy, the correctness of the experimental GC/MS chromatogram is verified, and the most possible cracking path is determined, and the results are consistent with the spectral analysis. It is due to the skeleton rearrangement reaction after α-cleavage, resulting in the formation of even electron ion fluorinated dimethyl silicon positive ion (m/z 77) and a neutral molecule. This not only verified the correctness of mass spectrogram analysis, but also showed the important role of skeleton rearrangement in the generation of m/z 77. Therefore, computational chemistry will be a more convenient, direct, accurate and systematic alternative to the effective implementation of analytical mass spectrometry reaction mechanism.