Sediment nitrogen and phosphorus pollution has become a critical factor limiting the sustained improvement of lake water quality in China. To address this issue, this study reviewed domestic and international literature and monitoring data from 2000 to 2022, obtaining surface sediment data from 131 lakes within China"s five major lake zones—Eastern Plain Lakes (EPL), Northeast Plain & Mountain Lakes (NPML), Inner Mongolia-Xinjiang Plateau Lakes (IXML), Yunnan-Guizhou Plateau Lakes (YGPL), and Tibetan Plateau Lakes (TPL). The Single Pollution Index (Pi) method was employed to evaluate the pollution status and spatial differentiation characteristics of Total Nitrogen (TN) and Total Phosphorus (TP). Furthermore, by incorporating case studies, this research systematically reviews the nearly 70-year evolution of management paradigms for lake sediments in China. The key findings are as follows: (1) TN pollution in lake sediments is relatively severe overall (Average Pi = 4.54), reaching a heavy pollution level, with a spatial pattern showing higher levels in the northeast and southwest and lower levels in central and western regions. The pollution degree across lake zones, in descending order, is: NPML Pi = 6.90 > YGPL (5.89) > IXML (5.08) > EPL (4.09) > TPL (4.08). In contrast, TP pollution is relatively lighter overall (Average Pi = 1.41), with the order YGPL Pi = 2.26 > NPML (1.96) > IXML (1.32) > EPL (1.27) > TPL (0.94), at a light pollution level. This indicates that the relatively severe TN pollution and the TP pollution in Chinese lakes are primarily influenced by localized anthropogenic inputs and regional natural backgrounds. (2) The management of sediment pollution in China has undergone a clear three-stage developmental progression: from engineering dredging (1950–1998) to environmental dredging (1998–2015), and then to the current stage of systematic governance (2015–present). (3) For future management, a systematic approach guided by the principle of "zoning, classification, and gradation" must be implemented. Efforts should focus on strengthening foundational surveys and database construction, promoting the classified recycling and utilization of sediments based on pollution characteristics, and establishing long-term guarantee mechanisms, to achieve effective internal pollution control and the long-term restoration of lake ecosystems in China.