In order to better understand the bioavailability, toxicity, migration and transformation behaviors of trace metals in river estuary, this study deeply investigated the interactions between organic matters in sediments and trace metals. The results suggested that both protein-like molecules and marine humic acids could react with trace metals (Cu2+ and Cd2+). These two fluorescent substances fixed trace metals through carboxyl group, hydroxyl group, and phenol hydroxyl group, and protein-like molecules were more sensitive than marine humic acids. Moreover, Cu2+ possessed stronger binding ability and more active sites with both protein-like molecules and marine humic acids. Hence, Cd2+ exhibited higher environmental risks due to the higher migration and transformation. The thermodynamic results revealed that the reaction between WEOM and trace metals was spontaneous and exothermic, and low temperature was favorable for immobilization of Cu2+ or Cd2+.This study could help to understand environmental behaviors and impact of trace metals on the sediments of Yangtze River estuary.