Lake ecosystem stability is a critical indicator of ecological health. To address limitations in existing assessment methods—including inadequate environmental representativeness and excessive data dependency—this study developed a Lake Ecosystem Stability Index grounded in the ecosystem stability framework proposed by Pararov et al. By incorporating lake-specific ecological characteristics and selecting representative indicators, the index integrates both structural and functional dimensions to quantify and compare stability across shallow lakes. The research integrates monthly phytoplankton and zooplankton biomass data from 2016 to 2021, quarterly data from 2022 to 2023, and meteorological and water quality data from Lake Hongze and Lake Luoma, along with monthly monitoring data from Lake Taihu from 2016 to 2023, to quantitatively assess the structural and functional stability of these lakes. The findings reveal: (1) Since 2020, the comprehensive structural stability index decreased from 0.567 ± 0.02 to 0.437 ± 0.04, while the functional stability index has remained stable, indicating that the functional stability of lake ecosystems generally surpasses structural stability(2) Comparative analysis revealed significantly higher ecosystem stability in Lake Taihu than in Lake Hongze and Lake Luoma.(3) Correlation analysis demonstrates that meteorological, water quality, and hydrological factors exhibit highly consistent associations with the structural and functional stability of Lake Hongze and Lake Luoma, but divergent patterns in Lake Taihu. Notably, nitrogen and phosphorus indicators in water quality exhibit the strongest correlations with the structural and functional stability of all three lakes. The dual-dimensional stability index proposed in this study offers a new perspective and quantitative approach for dynamic monitoring and assessment of lake ecosystem stability. It facilitates the identification of differences between structural and functional dimensions, and provides valuable reference for incorporating stability metrics into future lake health assessments and ecological restoration strategies.