Abstract: The distribution characteristics of Cu, Pb, Zn, Cd, Cr and As of 16 surface sediment samples from the Songhua River mainstream in September 2016 were studied. The pollution sources were investigated by factor analysis method, and the pollution level and ecological risk of these heavy metals in different river sections were assessed by geo-accumulation index and potential ecological risk index. The results showed that the total concentration of these heavy metals in the sample ranged from 43.46 to 311.23 mg/kg, which originated similarly from the mixed industrial, agricultural and domestic pollution in different mainstream sections. In the Nenjiang River mainstream and the Songhua River mainstream, the pollution level sequence was As>Pb>Cd>Cr>Cu>Zn, and in the Ersong River mainstream, the pollution level was As>Pb>Cd>Cr=Zn>Cu. The pollution level of As>Pb>Cd>Cr was observed in all sampled streams. In the sediments of the Nenjiang River, Ersong River and Songhua River mainstreams, the potential ecological risk sequence was As>Cd>Pb>Cu>Cr>Zn, and the potential ecological risk indexes were 46.5-209.2, 144.9-221.3 and 132.4-591.9 for the three river mainstreams, which means low, middle and middle potential ecological risk respectively.