Yangtze finless porpoises (Neophocaena asiaeorientalis asiaeorientalis), inhabiting the Yangtze River, are an endangered species in China. They are threatened by various kinds of pollutants, among which persistent organic pollutants (POPs) are of special concern due to their toxicities, high persistency and bioaccumulation potential. To better understand the POP contamination status of Yangtze finless porpoises, an investigation of stranded porpoises along the Yangtze River and adjacent two major lakes in the Yangtze River basin was conducted; the concentrations of four groups of legacy POPs, i.e., hexachlorocyclohexanes (HCHs), dichlorodiphenyltrichloroethanes (DDTs), polybrominated diphenyl ethers (PBDEs), and polychlorinated biphenyl (PCBs), were determined in the blubber samples. The mean concentrations of ΣHCHs (the sum of all congeners/isomers), ΣDDTs, ΣPBDEs and ΣPCBs, were 1670 ± 4210, 28,800 ± 52,300, 141 ± 174, and 1020 ± 1070 ng/g lipid weight, respectively; the high DDTs/PCBs ratio reflected a strong influence of agricultural pollution in the Yangtze River basin, and the high α/γ ratio of HCH isomers indicated the usage of lindane in the corresponding areas; the predominance of low-brominated congeners of PBDEs may be related to congruent patterns in the related environmental matrices. A hazard quotient risk assessment revealed that DDTs could pose a relatively high risk to Yangtze finless porpoises compared with the risks posed by the other POPs.