Geochemical behavior of major and trace elements in the sediment of the Songhua River was studied. 39 bottom sediment samples were collected from the Songhua River and total contents of As, Cd, Co, Cr, Cu, Hg, Zn, Ni, Pb, Sb, Sc, V, Mn, Ti, Al, Fe, Mg, Ca, Na and K in these samples were measured. The objectives of this study were to identify the contents and spatial variations of these metals in the sediment, investigate geochemical relationships among the elements, and develop baseline relationships between 9 trace metals and conservative reference element Sc to quantify the contamination of these 9 elements. Results indicated that the concentrations of toxic trace metals, such as As, Cd, Co, Cr, Cu, Hg, Zn, Ni, Pb, and V in the sediment, were 2.7-11.5, 0.05-1.38, 4.8-14.7, 15.9-78.9, 2.4-75.4, 0.01-1.27, 21.8-403.1, 6.2-35.8, 12.6-124.4, and 22.1-108.0 mg/kg, respectively. Due to the input of anthropogenic sources, temporal and spatial variation of Cd, Cu, Hg, Zn, and Pb contents in the sediment was higher than that of major elements. In addition, correlations between these metals and their mineral matrix elements such as Fe, Mg, and Sc were decreased. The baseline relationships between general metal contaminants and Sc were developed, with high correlation coefficients for Co, Cr, Cu, Zn, Ni, Pb, and V and relatively low correlation coefficients for As and Cd. These baseline relationships provide a way to quantitatively evaluate the sediment contamination by these metals. Generally, sediment contamination of the Songhua River by trace metals was less than that of the Zhujiang River and the Changjiang River, and similar to that of the Huanghe River.