Polybrominated diphenyl ethers (PBDEs) and dechlorane plus (DP) are two kinds of widely used organic flame retardants, and PBDE and DP residues have been found in both environment and biota. A method for the determination of 8 PBDEs and 2 DPs in fish and fish oil supplements was developed using auto gel permeation chromatography (GPC) coupled with gas chromatography-negative chemical ionization/mass spectrometry (GC-NCI/MS) in the selected ion-monitoring (SIM) mode on a 15 m capillary column. The sample added with BDE-77 and 13C12-BDE-209 as the internal standards was extracted using a Soxhlet extractor, and further purified by auto GPC and a multilayer silica gel column. The sample preparation procedure was optimized, and the characteristic ions and fragmentations of the analytes in NCI/MS were studied. The limits of detection (LODs, S/N = 3) ranged from 2.2 to 39.8 ng/kg. The average recoveries were between 71.1% and 121.4% at two spiked levels of 2 and 20 ng/g for both BDE-209 and DP and 0.2 and 2 ng/g for others with the relative standard deviations between 2.96% and 13.31%. The developed method has been successfully applied in the determination of PBDEs and DPs in several fish and fish oil supplements samples. The total PBDEs found ranged from 2.18 to 15.93 ng/g, and DP was not found. This method was validated to be accurate and sensitive for the trace analysis of PBDEs and DPs in the samples with fat.