The detection method of carbonyl compounds (CCs) in the atmosphere has been a challenging problem because of its low concentration and strong volatility and reactivity. Based on the existing thermal desorption (TD) technology, the TD instrument was combined with gas chromatography/mass spectrometry (GC/MS), and pentafluorophenyl hydrazine (PFPH) was used as derivatization reagent to establish a simple, high sensitivity, good stability and simultaneous detection of 13 atmospheric carbonyl compounds, namely PFPH derivation-two-stage TD-GC/MS analysis method. The main factors affecting the TD conditions were discussed, including desorption temperature, desorption time and carrier gas flow rate. The results showed that when the tube desorption flow rate and time were 10 mL min−1 and 8 min, and the trap desorption flow rate and time were 5 mL min−1 and 8 min, the recoveries of various CCs PFPH-derivatives were relatively high. The collection efficiencies of all detected carbonyls by this method were above 85 %. The method detection limits (MDLs) of the tested carbonyls were in the range of 0.44–1.23 ng cartridge−1. Compared with the method of PFPH-solvent desorption-GC/MS, the two-stage TD-GC/MS method showed lower MDLs and more carbonyls detected at low concentrations. In brief, the two stage TD-GC/MS analysis method is of great significance for the detection of trace CCs in the time-varying atmospheric environment, and is worthy of popularization and application in atmospheric samples.