The Yellow River contains large amounts of sands, resulting in a peculiar hydraulic condition which is characterized by a magnificent interface between the particulates and water. In addition, Baotou section of the Yellow River suffers from severe heavy metal pollution receiving the industrial discharges from the Baotou city. Therefore, this study was carried out on Baotou section of the Yellow River based on its representativeness on the mechanism of heavy metal adsorption on water-sediment interface, and on the heavy metal spatial distribution, mobilization, transformation, and accumulation effects in sediments. Based on the theories and methods of environmental geochemistry, biogeochemistry, pollution ecology and modern sedimentology, the speciation distribution characters of heavy metals such as Cu, Pb, Zn in the different grain sizes sediments and the contribution of the different grain sizes sediments on the concentrations of different heavy metals speciation were discussed in this work. The results indicated that the bound to Fe-Mn oxide was the dominant form of non-steady-state of Cu, Pb, and Zn in different grain sizes sediments from the Yellow River.