Abstract: Xingkai Lake is the largest international cross-border lake in China. The water quality of Xingkai Lake has attracted international attention. The release of sediment internal pollution is an important factor affecting water quality. Studying the distribution characteristics and sources of sediment nutrients can provide important support for the water environment management of Xingkai Lake. Small Xingkai Lake and Great Xingkai Lake in China were investigated. Firstly, the distribution characteristics and burial fluxes of total nitrogen (TN), total phosphorus (TP) and organic matter (OM) in the sediments were clarified through the investigation of sediment nutrients and accumulation of sediment. Subsequently, the organic pollution index method was used to evaluate the sediment pollution level of Xingkai Lake. Additionally, nutrient sources were analyzed based on C/N and C/P values. The results showed that compared with other lakes in China, the average concentration of TP in the sediment of Xingkai Lake was at a low level, while the average concentrations of TN and OM in the sediment of Small Xingkai Lake were at a high level. The nutrient concentration was higher in the west and northeast of Small Xingkai Lake with high coverage of aquatic plants, and in the west and middle of Great Xingkai Lake with serious sediment deposition. The OM in the sediments was influenced by both aquatic plants and terrestrial inputs, and Small Xingkai Lake was more affected by terrestrial inputs. Pearson correlation analysis showed that OM and TN were homologous and not homologous with TP. The organic pollution evaluation results presented that Xingkai Lake was in light pollution, while the organic pollution in Small Xingkai Lake was more serious than that in Great Xingkai Lake. In conclusion, Small Xingkai Lake, as the front lake of Great Xingkai Lake, reduced the pollutants imported into Great Xingkai Lake. However, its high sediment nutrient concentrations may have a potential impact on Great Xingkai Lake. Therefore, attention should be paid to the sediment pollution of Small Xingkai Lake.