Contents of 26 heavy metals in the 39 offshore surface sediments of Jiulong River were determined by inductively coupled plasma mass spectrometry(ICP-MS), atomic fluorescence spectrometry(AFS) and atomic absorption spectrometry(AAS). Geo-accumulation index and potential ecological risk index were applied to evaluate the pollution degree and potential ecological risk of heavy metals, and multivariate statistical methods were applied to speculate the main sources of these heavy metals. The results showed that the distributions of heavy metals were different in three regions of Jiulong River(north creek, western creek and estuary), the high contents of Mn, Zn, Cd, Mo, Sb, Cs, Y, Th and U elements appeared in the north creek and western creek, and the high contents of Fe, Ni, Cr, V, Co, Sc, Li, Rb, Sr, Tl and Ga elements appeared in the estuary. Most of these elements were enriched in the sediments. The results of pollution assessment by geo-accumulation index revealed that the pollution degree of Cd was the highest and at a serious polluted level in 10.3% of the samplings. The assessment results of potential ecological risk indicated that the potential ecological risk of heavy metals showed the order of Cd >Hg >Cu >Pb >Ni >Co >Cr >Mn >Zn >V. Cd and Hg contributed the most to the total potential ecological risk, accounting for 78.1% and 12.1%, respectively. The results of multivariate statistics analysis indicated that the source of Fe, Mn, Zn, Pb, Cu, Cr, Cd, Hg, Mo, Sb and Bi were mainly from agricultural activities and mining activities; the source of Ni, Co, Sc, Li, Rb, Sr, Be, Ga and Tl were mainly from burning fossil fuels; and the source of Ba, Y, V, Th, U and Cs were mainly from the rock weathering of granite.