C, N, and P in lake sediment are the basis of material and energy cycle, reflecting the economic development, ecological function, and environmental effect. Current research on the effect of lake eutrophication on carbon storage and the river-lake connectivity on nutrient diffusion is lack. This work investigated the accumulation, distribution, correlations, and stoichiometric ratios of C, N, and P of 82 lakes (≥ 10km2) in Eastern China, analyzed the nutrient limitation, sediment carbon sink, and effect of river-lake connectivity, and discussed the relationships between eutrophication and sediment carbon storage. The average concentrations and ranges of total C, N, and P in lake sediments were (23.26mg/g, 0.08-153.45mg/g), (2.32mg/g, 0.29-14.17mg/g), and (0.86mg/g, 0.23-2.64mg/g), respectively. The ecological stoichiometry of C: N: P in lake sediments was 32: 3.2: 1. P can be easily accumulated in lakes connected from the Yangtze River, while C and N can be easily accumulated in disconnected lakes. The soil-water erosion in runoff is an important factor for P diffusion. The C/N and C/N/P weren't affected by the river-lake connectivity but depended on the plant type. The Eastern Plain Lake Region of China is C and N co-depletion, and P enrichment. The lake eutrophication leading to algal bloom is unfavorable to the goal of carbon storage and carbon neutrality. Outcome of this study will provide a significant reference and strategies for carbon sequestration research, eco-environmental protection, and watershed nutrient management.