Polybrominated diphenyl ethers (PBDEs) are highly lipophilic compounds with high toxicity and long-term bioaccumulation, which have strong affinities to suspended particulates in water. So PBDEs are easily adsorbed to sediments, and cause potential risks to human beings and aquatic ecosystem. In order to investigate the levels and patterns of PBDEs in the Yangtze River, 13 surface sediment samples were collected from the middle reaches of the regions and the concentrations of 9 PBDE congeners in the sediments were determined using High Resolution Gas Chromatography/High Resolution Mass Spectrometry (HRGC/HRMS). The total concentrations of PBDEs ranged from 46.1 to 326 pg · g⁻¹ dry weight. BDE-99 and BDE-47 were the dominant PBDE congeners, which averagely contributed 51.6% and 19.6%, respectively. The concentrations of PBDEs were relatively low compared to those in other studies. The total organic carbon (TOC) was also analyzed in this study, and the results indicated that there was no obvious positive correlation between the levels of PBDEs and TOC. In addition, based on the PBDEs concentration levels, the ecotoxicological risks of PBDEs contamination in surface sediments of the Yangtze River were evaluated by the quotient method. The results showed that the levels of PBDEs were considerably low and these compounds should have no risk to human health.