In order to identify the source of heavy metals and quantify their contributions, surface sediment of Lake Poyang during the wet season were selected as the research object, and the contents of 14 heavy metals (V, Cr, Co, Ni, Cu, Zn, Sr, Mo, Cd, Sb, W, Pb, Hg and As) were determined. The pollution and spatial distribution characteristics of 14 heavy metals were analyzed, and the principal component analysis (PCA) and positive definite matrix factorization (PMF) were applied to apportion the sources of sediment heavy metals. The results showed that except for V and Cr, the average contents of Cd, Mo, Hg, Cu, Pb, Zn, W, Sr, As, Ni, Co and Sb were 5.7, 2.2, 1.9, 1.8, 1.5, 1.5, 1.4, 1.3, 1.3, 1.2, 1.0 and 1.0 times of their respective soil background values of Jiangxi Province. The exceeding rates of Cd, Hg, Cu, Mo, Pb, Sr and Zn were relatively high, there were 100%, 100%, 100%, 100%, 97%, 97% and 93% of sediment samples with higher Cd, Hg, Cu, Mo, Pb, Sr and Zn contents than their respective soil background values of Jiangxi Province, respectively. And 51% of sediment samples had higher Cd contents than the risk screening values for soil contamination of agricultural land. V, Cr, Co, Ni, Cu, Zn, Sr, Mo, Sb, W, Pb, Hg and As were at unpolluted to minimal contamination levels, while Cd displayed moderate contamination level, closed to heavy contamination level. Overall, the pollution of Cd was relatively serious. The distribution of heavy metals had significant regional characteristics. The spatial distributions of Cr, Cu, Zn, Sr, Pb, Hg and As were very similar, showing the high content values were clustered near the river inlets of Ganjiang, Fuhe, Xinjiang, Raohe, while Co, Ni, Mo and Sb were obviously concentrated in the southern of lake region, the northeast region and the Xiushui into the lake. The spatial variability of Cd and W was relatively large, while the contents of V were relatively uniform. Source apportionment results of PCA and PMF indicated that the heavy metals in surface sediments from Lake Poyang during the wet season were affected by four sources. Mining and industrial activities, tailings and waste residue, agricultural activities were identified as the main anthropogenic sources for sediment heavy metals in this study area, accounting for 38%, 28% and 19% of the total contribution, respectively. The remainder was the natural source, accounting for 14% of total contribution.