Concentrations of dissolved Cd, Cu, and Zn, and Cu-binding organic ligands in the waters of the Kuroshio region in the East China Sea were presented in this dataset. The samples were collected as part of the GEOTRACES-Japan project during KH-15-3 cruise (Principal Investigator: Jing Zhang, Toyama University, Japan) onboard R/V Hakuho Maru in October 2015 to understand trace element distributions and behaviors in the highly dynamic East China Sea. All sampling followed trace-metal clean techniques as stated in the GEOTRACES cookbook. Seawater samples were filtered through 0.2 μm filter and acidified for dissolved trace metal analysis or frozen for organic ligand analysis. Trace metal concentrations were measured using ICP-MS following pre-concentration by NOBIAS PA-1 chelating resin column, while the chemical speciation parameters of Cu were determined using competitive ligand exchange adsorptive cathodic stripping voltammetry with salicylaldoxime as the competing ligand. These data reveal the unique interaction between the continental shelf waters and Kuroshio waters in the East China Sea.