Eutrophication of lakes exhibits a more serious trend in a global scale under the climate change. Eutrophic lakes also exhibit a unique role in global carbon, yet, data on carbon dioxide (CO2) emissions from these eutrophic lakes are too scarce to accurately upscale CO2 emissions for large scale or global estimation. This study presented the results of a partial pressure of carbon dioxide (pCO2) survey covering 43 eutrophic lakes in China in the same season across diverse ecosystem types and climate zones. The first estimation of CO2 flux from Chinese eutrophic lakes was reported as − 0.7 to 1.0 Tg C a−1 based on the surveyed pCO2 values, indicating some lakes act as CO2 sinks while others are sources. The results showed that pCO2 in Chinese eutrophic lakes ranged from 0.9 to 1366.4 μatm with the mean of 356.9 ± 310.3 μatm, almost 69.3 % of the sampling sites in eutrophic lakes were undersaturated with CO2 to the atmosphere. The mean pCO2 variations in eutrophic lakes were consistent with the amount of precipitation across different climate zones, with the trend of semiarid > semihumid > humid regions, and all lower than that for atmosphere. Meanwhile, both the mean and median values of pCO2 went down with the decrease of the lake mean depth and the increasing lake area, and the highest value in deep lakes (mean depth > 10 m, 548.3 ± 353.7 μatm) and small lakes (376.6 ± 329.8 μatm). In all the studied eutrophic lakes, pCO2 values showed significant seasonal variations, and in summer and autumn showed an under-saturated seasonal mean value. This study proved that CO2 undersaturation was prevalent in the eutrophic conditions. Due to the CO2 source-sink conversion role of eutrophic lakes, it is recommended to focus on CO2 fluxs from eutrophic lakes in the first place during the research of inland waters carbon emissions.