The pollution status of polychlorinated naphthalenes (PCNs) in the sediment of the Yangtze River Basin, Asia’s largest river basin, was estimated. The total concentrations of PCNs (mono- to octa-CNs) ranged from 0.103 to 1.631 ng/g. Mono-, di-, and tri-PCNs—consisting of CN-1, CN-5/7, and CN-24/14, respectively, as the main congeners—were the dominant homolog groups. Combustion indicators and principal component analysis showed that the emissions from halowax mixtures were the main contributor to PCNs in sediment, among most of the sampling sites. The mean total toxic equivalent (TEQ) was calculated to be 0.045 ± 0.077 pg TEQ/g, which indicates that the PCNs in sediments were of low toxicity to aquatic organisms. This work will expand the database on the distribution and characteristics of PCNs in the river sediment of China.