Nine units in new-born intertidal zone of the Yellow River estuary, China were examined for concentrations of heavy metals (Pb, Cr, Cu, Zn and Ni) in sediments and plants. Heavy metal levels in surface sediments were in the order of Zn>Pb≈Cr>Cu≈Ni and generally increased in a seaward direction except for Z6 (Tamarix chinensis-Suaeda salsa zone) and Z7 (S. salsa-T. chinensis zone) units. Significant differences in metal concentrations of the 9 units were observed in the profiles (p<0.01). Heavy metal levels in the shoots or roots of different plants decreased in the order of Zn>Cu>Pb>Ni>Cr and differed among plants or tissues. The roots at Z2 (Calamagrostis pseudophragmites zone), Z3 (Imperata cylindrical zone) and Z4 (Phramites australis zone) units accumulated greater metals than shoots TFs (translocation factors)<1, while the shoots at Z1 (Sparganium minimum-Potentilla supina zone), Z7 and Z8 (S. salsa zone) units accumulated greater metals than roots (TFs>1), implying that intertidal plants showed different pathways in metal accumulation and internal transportation. Except for Pb, the concentrations of Cr, Cu, Zn and Ni in sediments were lower than the criteria of Class I recommended by the Environmental Quality Standard for Soils of China. Although heavy metal levels in intertidal zone were generally the lowest (Cr, Cu, Zn and Ni) or relatively moderate (Pb) compared with other estuaries or bays in Asia and Europe, high eco-toxic risk of Pb and Ni exposure still could be observed at Z4, Z6 and Z9 (mudflat zone) units. S. salsa was more suitable for the potential biomonitor or phytoremediation of all five heavy metals if intertidal sediments was seriously contaminated with increasing of pollutants loading in the Yellow River estuary. •Significant differences in heavy metal concentrations of the 9 units occurred in the profiles.•Heavy metal concentrations in sediments were related to pollutant inputs, grain-size and SOM.•Intertidal plants showed different pathways in metal accumulation and internal transportation.•Intertidal zone (Z4, Z6 and Z9 units) showed high eco-toxic risk of Pb and Ni exposure.•Suaeda salsa was more suitable for the potential biomonitor or phytoremediation of heavy metals.