Nonhydrolyzable organic carbon (NHC) and sorption isotherms of phenanthrene (Phen) on six size-fractionated NHC fractions in two sediments from the Pearl River and Estuary, South China, were investigated. It was found that NHC including ancient organic carbon, black carbon, resistant aquatic organic carbon, and aged soil organic carbon consists mainly of aliphatic and aromatic carbon using 13C nuclear magnetic resonance spectroscopy. The sorption isotherms of Phen by the size-fractionated NHC fractions are nonlinear and are well-fitted to the Freundlich model. For the estuary sediment, the NHC contents and the organic carbon-normalized distribution coefficients (Koc) in the size fractions increase with decreasing particle size. The clay NHC fraction contributes to 70% of the Phen sorption by the bulk NHC isolate. However, for the contaminated river sediment, the NHC contents and the Koc values exhibit no regular variations among the size fractions. The Phen sorption capacities on the size-fractionated NHC fractions of the two sediments are significantly related to their H/C ratios and aliphatic carbon, but negatively to aromatic carbon. The fine-particle NHC fractions with high aliphatic carbon and H/C ratio play a very important role in the sorption, transport, and fate of Phen by the investigated sediments.