This paper discussed the pollution characteristics and their sources of Hg, Cd, Cr, As and Pb in the bottom sediments of Songhua River in the Hakanson's Potential Ecological Risk Index Method (RI) and Principal Component Analysis (PCA) to reveal the metal pollution status of the whole Songhua River, which is the biggest tributary of the Heilongjiang River at the China-Russian border. The results showed that: the concentration order from high to low by average was wCr>wPb>wAs>wCd>wHg; the coefficient of variation (CV) revealed that the spatial distribution of Hg and As was discrete and Cd and Pb were homogeneous. In the method of PCA, the main sources of heavy metal pollutants were inferred. The Eri of Hg and Cd was higher，and the RI analysis uncovered that the potential ecological risk declined compared with the past, and just the 4 sections of 1#，2#, 7# and 10# were in moderate level only.