Abstract: 11 representative polybrominated diphenyl ethers (PBDEs) were analyzed based on the gas chromatography-electron capture detector method, and the effects of different types of gas chromatographic columns on the separation and analysis of PBDEs were investigated. The results showed that the polarity of column is the key factor affecting the separation and response. On the stationary phase with stronger polarity, the retention time of each PBDEs monomer became longer and the response decreased, especially the response of highly substituted PBDEs was most affected. The column length and thickness stationary phase also have significant effects on the PBDEs analysis. Short column with thin stationary phase were suitable for the analysis of 11 PBDEs. Different brands of columns were affected by the production process and have a greater effect on the response to PBDEs.