Under the combined pressures of climate change and human activities, lake ecosystems across different regions of the Poyang Lake Basin have experienced varying degrees of degradation. A deep understanding of the long-term evolution and pattern of the lake basin environment is of great significance for the ecological restoration and conservation of Poyang Lake. Based on 21?Pb dating, this study employs a multi-proxy analysis including total organic carbon (TOC), total nitrogen (TN), their molar ratio (C/N ratio), organic carbon accumulation rate (OCAR), total nitrogen accumulation rate (TNAR), and stable carbon isotope of organic matter (δ13C??g) in sediments from Junshan Lake and Qinglan Lake in the southern Poyang Lake basin. It reveals the main sources of sedimentary organic matter and potential mechanisms driving changes in lake primary productivity and eutrophication processes over the past century. The results indicate that the C/N ratios and δ13C??g values in Junshan Lake ranged from 7.7 – 10.5 and -23.9‰ to -22.0‰, respectively, while in Qinglan Lake they ranged from 8.7 – 11.3 and -26.3‰ to -21.7‰. This suggests that sedimentary organic matter in both lakes primarily originated from macrophytes (large aquatic plants) and phytoplankton. Post-1905 in Junshan Lake and post-1980 in Qinglan Lake, TOC and TN concentrations showed an increasing trend, reflecting a common characteristic of gradually rising lake primary productivity. The differences in the response of δ13Corg to changes in primary productivity of different types of lakes reflected the differences in the composition of aquatic plant communities. Specifically, Junshan Lake, primarily influenced by climate warming and aquaculture activities, has undergone a successional shift over the past two centuries: from macrophyte dominance, through a phase of macrophyte-algae codominance, to the current state of algal dominance. In contrast, Qinglan Lake experienced a decline in submerged vegetation following the diversion of the river in 1958, largely due to increased sediment input. After 1980, superimposed impacts from domestic sewage and agricultural non-point source pollution associated with urbanization further accelerated this trend. Consequently, phytoplankton has become the dominant source of sedimentary organic matter in Qinglan Lake. Furthermore, this study compares the ecological environment evolution in different sub-regions of Poyang Lake, providing a scientific basis for understanding their divergent characteristics and clarifying the mechanisms of ecological degradation driven by the coupling of multiple factors.