Information about the occurrence and trophic transfer of polychlorinated naphthalenes (PCNs) in polar ecosystems is vital but scarce. In this study, PCNs were analyzed in benthic marine sediment and several biological species, collected around the Chinese polar scientific research stations in Svalbard in the Arctic and South Shetland Island in Antarctica. Total PCNs in biota ranged from 28 to 249 pg/g of lipid weight (lw) and from 11 to 284 pg/g lw in the Arctic and Antarctic regions, respectively. The concentrations and toxic equivalent (TEQ) of PCNs in polar marine matrices remained relatively low, and the compositions were dominated by lower chlorinated homologues (mono-to trichlorinated naphthalenes). Trophic magnification factors (TMFs) were calculated for congeners, homologues, and total PCNs in the polar benthic marine food webs. Opposite PCN transfer patterns were observed in the Arctic and Antarctic regions, i.e., trophic dilution and trophic magnification, respectively. This is the first comprehensive study of PCN trophic transfer behaviors in remote Arctic and Antarctic marine regions, providing support for further investigations of the biological trophodynamics and ecological risks of PCNs.