The Earth has undergone a significant climate switch from greenhouse to icehouse during the Plio–Pleistocene transition (PPT) around 2.7–2.4 million years ago (Ma), marked by the intensification of the Northern Hemisphere glaciation (NHG) ~2.7 Ma. Evidence based on oceanic CO2 [(CO2)aq], supposed to be in close equilibrium with the atmospheric CO2 [(CO2)atm], suggests that the CO2 decline might drive such climate cooling. However, the rarity of direct evidence from [CO2]atm during the interval prevents determination of the atmospheric CO2 level and further assessment on the impact of its fluctuation. Here, we reconstruct the [CO2]atm level during 2.77–2.52 Ma based on a new developed proxy of stomatal index on Typha orientalis leaves from Shanxi, North China, and depict the first [CO2]atm curve over the past 5 Ma by using stomata-based [CO2]atm data. Comparisons of the terrestrial-based [CO2]atm and the existed marine-based [CO2]aq curves show a similar general trend but with different intensity of fluctuations. Our data reveal that the high peak of [CO2]atm occurred at 2.77–2.52 Ma with a lower [CO2]aq background. The subsequent sharp fall in [CO2]atm level might be responsible for the intensification of the NHG based on their general temporal synchronism. These findings shed a significant light for our understanding toward the [CO2]atm changes and its ecological impact since 5 Ma.