A method has been developed for gas chromatographic peak recognition of polybrominated diphenyl ethers (PBDEs) under different temperature programs. On the basis of an identification database of retention parameters (A, B values) of gas chromatography and retention times of the selected internal standards, the retention times of BDEs can be accurately estimated. In comparison with the experimental retention values, the predicted retention times have been proved to be very accurate. In addition, owing to only a part of BDE analytical standards are available, using 40 BDEs as a training set, the quantitative relationship between retention parameters of BDEs and molecular connectivity indexes has been found. The correlation coefficients are greater than 0.997. The A, B values of all the remaining 169 BDE congeners have been predicted.