The Second Songhua River was subjected to a large amount of raw or primary effluent from chemical industries in Jilin city in 1960s to 1970s, resulting in serious mercury pollution. However, an understanding of other trace metal pollution has remained unclear. The objective of this study was to investigate trace metal contamination in the sediment of the river. Bottom sediment samples were taken in the river between Jilin city and Haerbin city in 2005. An uncontaminated sediment profile was taken in the Nen River at the same time. Total concentrations of Al, Fe, Mg, Ca, K, Na, Ti, Mn, V, Sc, Co, Cu, Cr, Ni, Pb and Zn in the sediment samples were measured by ICP-MS or ICP-OES, following digestion with various acids. Concentrations of Co, Cu, Cr, Ni, Pb and Zn in the surface sediments were 5.1-14.7, 18.5-78.9, 2.4-75.4, 7.2-29.0, 13.5-124.4, and 21.8-403.1 mg/kg, respectively, generally decreasing along the course of the river from Jilin city to Haerbin city. Background concentrations of trace metals were reconstructed by geochemical normalization to a conservative element scandium. Results showed that concentrations of Co, Cr, and Ni in the sediment were generally only slightly higher than or equal to their background values, while concentrations of Cu, Pb, and Zn in the some sediment samples were significantly higher than their background values. In detail, the sediment at Jilin city was moderately contaminated by Cu, and the sediment of the Second Songhua River was moderately contaminated by Pb and Zn. The top layer (0-10 cm depth) and bottom layers (30-46 cm depth) of one sediment profile at Wukeshu town were generally moderately polluted by Pb and Zn. Synthetically, the surface sediment in the studied river section was classified as natural sediment without ecological risk by the sediment pollution index (SPI) of Cu, Cr, Ni, Pb and Zn. Only the 30-45 cm depth of the sediment profile at Wukeshu town was classified as low polluted sediment by the SPI of these metals, recording a historical contamination of the river in the 1960s to 1970s. This buried contamination of trace metals might pose a potential risk to water column under disturbance of sediment.