The spatiotemporal variability of lake partial carbon dioxide pressure (pCO2) introduces uncertainty into CO2 flux estimates at the lake water-air interface. Knowing the variation pattern of pCO2 is important for obtaining accurate global estimation. Here we examine seasonal and trophic variations in lake pCO2 based on 13 field campaigns conducted in Chinese lakes from 2017 to 2021. We found significant seasonal fluctuations in pCO2, with decreasing values as trophic states intensify within the same region. Saline lakes exhibit lower pCO2 levels than freshwater lakes. These pCO2 dynamics result in variable areal CO2 emissions, with lakes exhibiting different trophic states (oligotrophication > mesotrophication > eutrophication) and saline lakes differing from freshwater lakes (−23.1 ± 17.4 vs. 19.3 ± 18.3 mmol m−2 d−1). These spatiotemporal pCO2 variations complicate total CO2 emission estimations. Using area proportions of lakes with varying trophic states and salinity in China, we estimate China's lake CO2 flux at 8.07 Tg C yr−1. In future studies, the importance of accounting for lake salinity, seasonal dynamics, and trophic states must be noticed to enhance the accuracy of large-scale carbon emission estimates from lake ecosystems in the context of climate change.