Stable isotope method serves as an important means to uncover the ecosystem structure and functioning, and to reveal the composition of lake food webs and the processes for biogeochemical cycling. In this study, a spatial survey of ten lakes with different nutrient levels in Eastern Yunnan was conducted through analyzing the carbon and nitrogen stable isotopes and elemental composition for aquatic plants (submerged macrophyte, floating plant), phytoplankton and zooplankton, respectively. The result shows that, among the four groups of lake organisms, floating plant has the most negative signal of stable carbon isotope, with a mean value (±SD) of -28.99‰±0.86‰. While phytoplankton (-21.88‰±2.97‰) and zooplankton (-20.85‰±2.70‰) are characterized by similar carbon isotope values, the submerged macrophyte has a large variation with significantly more positive δ¹³C value (-12.04‰±4.57‰). This indicates that the difference in carbon sources absorbed or utilized has caused the deviation in stable carbon isotope composition among these four organisms. In terms of stable nitrogen isotope, the primary producers, including submerged macrophyte (5.43‰±5.84‰), floating plant (5.58‰±7.38‰) and phytoplankton (7.26‰±3.83‰), show significantly similar δ¹⁵N values. While the δ¹⁵N value of primary consumer, zooplankton (11.02‰±3.18‰), is significantly higher with a averaged enrichment factor by 3.46‰, indicating the effect of nitrogen isotope fractionation across trophic levels in our lakes. Furthermore, the carbon isotope signal of lake organisms are also affected by factors such as water temperature and water depth. The variation in the nitrogen isotope signal is dominated by lake eutrophication, which leads to a gradual enrichment in the organismal signal of δ¹⁵N. In addition, the carbon and nitrogen content of aquatic organisms from Yunnan lakes are higher than those in lakes from the middle and lower reaches of the Yangtze River. There existed a threshold C/N ratio of primary producers and primary consumers in defining the shift between autochtonous and allothonous sources of organic matter in our lakes. This spatial survey provided important data for understanding the food web composition and biochemical cycling for plateau lakes.