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Abstract Background It is important to quantify changes in CO2 sources and sinks with land use and land cover change. In the last several decades, carbon sources and sinks in East Asia have been altered by intensive land cover changes due to rapid economic growth and related urbanization. To understand impact of urbanization on carbon cycle in the monsoon Asia, we analyze net CO2 exchanges for various land cover types across an urbanization gradient in Korea covering high-rise high-density residential, suburban, cropland, and subtropical forest areas. Results Our analysis demonstrates that the urban residential and suburban areas are constant CO2 sources throughout the year (2.75 and 1.02 kg C m−2 year−1 at the urban and suburban sites), and the net CO2 emission indicate impacts of urban vegetation that responds to the seasonal progression of the monsoon. However, the total random uncertainties of measurement are much larger in the urban and suburban areas than at the nonurban sites, which can make it challenging to obtain accurate urban flux measurements. The cropland and forest sites are strong carbon sinks because of a double-cropping system and favorable climate conditions during the study period, respectively (− 0.73 and − 0.60 kg C m−2 year−1 at the cropland and forest sites, respectively). The urban area of high population density (15,000 persons km−2) shows a relatively weak CO2 emission rate per capita (0.7 t CO2 year−1 person−1), especially in winter because of a district heating system and smaller traffic volume. The suburban area shows larger net CO2 emissions per capita (4.9 t CO2 year−1 person−1) because of a high traffic volume, despite a smaller building fraction and population density (770 persons km−2). Conclusions We show that in situ flux observation is challenging because of its larger random uncertainty and this larger uncertainty should be carefully considered in urban studies. Our findings indicate the important role of urban vegetation in the carbon balance and its interaction with the monsoon activity in East Asia. Urban planning in the monsoon Asia must consider interaction on change in the monsoon activity and urban structure and function for sustainable city in a changing climate.