Abstract: In this paper, the element compositions and the geochemical characteristics of the clay-sized sediments of the Yangtze and Yellow Rivers estuaries were studied. It is found that the sediments in the Yangtze River is relatively rich in major elements Al, K, Fe, Ti and trace elements Cr, V, Li, Zn, Ni, Rb, whereas the Yellow River sediments characterized by Ca, Sr and Ba. As far as the rare earth elements are considered, the sediments from the Yangtze River contain more rare earth elements (REEs) with same fractionation degree comparing to those from the Yellow River. Chondrite standardized curve of rare earth elements reveals a pattern of LREE enrichment and HREE heavy loss in a slightly right-wing type. In the standardized distribution model by the upper continental crust, medium REEs are enriched. However, the negative Ce anomaly and the positive Eu anomaly of the Yellow River sediments are smaller than those in the Yangtze River sediments. The content of elements in the sediments of the Yangtze River varies greatly. Instead it is relatively concentrated in the Yellow River sediments. RERs, ΣREE, δCe of clay-sized sediments are closer to the source rocks and can be used as a geochemical indicator to distinguish the sediments of the Yangtze River from the sediments of the Yellow River. The geochemical characteristics of clay-sized sediments from the Yangtze and Yellow Rivers are controlled by lithology, chemical weathering and hydrodynamic sorting in the source area. Chemical weathering caused the geochemical differentiation of river sediments starting from the source, and the hydrodynamic environment contributed to the differentiation and separation of minerals of different sizes in the transportation.