Limited field samplings result in significant uncertainties in regional and global estimates of lake carbon dioxide (CO2) emissions. However, quantitative analysis of uncertainty in regional lake CO2 emission estimates remains unclear. In this study, we utilized satellite data to estimate carbon dioxide flux from 113 eastern China lakes, revealing substantial spatial and temporal variations in flux, averaging 18.07 ± 81.83 mg m−2 d−1. Additionally, satellite-estimated total CO2 effluxes indicated previous upscaling studies had overestimated total CO2 effluxes from these studied lakes by approximately 3–11 times, primarily due to substantial variations in lake CO2 fluxes. Insufficient sampling resolution resulted in considerable uncertainty in upscaling estimations. Temporal variations in carbon dioxide contributed greater upscaling uncertainties than spatial variations in carbon dioxide. To capture the dynamics of lake CO2, increasing the number of sampling points and events is necessary as lake size decreases and trophic state increases. Finally, we propose a prediction for the optimal sampling resolution based on lake area and trophic state, recommending an average of 5 points per lake and bi-monthly sampling as the ideal resolution for similar shallow eutrophic lakes. This approach has been validated as effective in lakes across North America and Europe. We believe that future global-scale lake carbon budget estimates would benefit from field observations conducted at more reasonable sampling points and frequency.