Land use change and fossil fuel consumption due to urbanization have made significant effect on global carbon cycle and climate change. Accurate estimating and understanding of the carbon budget and its characteristics are the premises for studying carbon cycle and its driving mechanisms in urban system. Based on the theory of eddy covariance (EC) technique, the characteristics atmospheric boundary layer and carbon cycle in urban area, this study systematically reviewed the principles of CO_2 flux monitoring in urban system with EC technique, and then summarized the problems faced in urban CO_2 flux monitoring and the method for data processing and further assessment. The main research processes on urban carbon fluxes with EC technique were also illustrated. The results showed that the urban surface was mostly acting as net carbon source. The CO_2 exchange between urban surface and atmosphere showed obvious diurnal, weekly and seasonal variation resulted from the vehicle exhaust, domestic heating and vegetation respiration. However, there still exist great uncertainties in urban flux measurement and its explanation due to high spatial heterogeneity and complex distributions of carbon source /sink in urban environments. In the end, we suggested that further researches on EC technique and data assessment in complex urban area should be strengthened. It was also requisite to develop models of urban carbon cycle on the basis of the system principle, to investigate the influencing mechanism and variability of urban cycle at regional scale with spatial analysis technique.