Emerging brominated flame retardants (eBFRs) other than polybrominated diphenyl ethers (PBDEs), polybrominated biphenyls (PBBs) and their derivatives in foods have been in focus in recent years due to their increasing production volumes, indefinite information on toxicities and the lack of data on occurrence in environments, foods as well as humans. In this study, gas chromatography was coupled to an atmospheric pressure chemical ionization-tandem mass spectrometry (APGC-MS/MS) for the analysis of six eBFRs in pork, chicken, egg, milk and fish. A short section of unpacked capillary column coupled to the end of the analytical column was applied to improve the chromatographic behaviors of high boiling point compounds. The method was comprehensively validated with method limit of quantification (mLOQ) lower than 8 pg/g wet weight (w.w.). Samples from Chinese Total Diet study were quantified following the validated APGC-MS/MS method. 2,3,4,5-pentabromo-6-ethylbenzene (PBEB), hexabromobenzene (HBB), pentabromotoluene (PBT) and 1,2-bis(2,4,6-tribromophenoxy)ethane (BTBPE) were most frequently detected in samples. The highest concentration was found in fish with 351.9 pg/g w.w. of PBT. This is the first report on the presence of PBT in food samples with non-ignorable concentrations and detection rate.