Abstract: The agricultural soil carbon dynamic process and its regulatory mechanism helps inform better understanding of terrestrial carbon cycle processes and global carbon balance estimates. Stable carbon isotope as a natural tracer has many advantages over radioisotope techniques such as safety, no pollution and high controlability, and has been widely used in the soil carbon cycling research in agricultural ecosystems. Investigation of the carbon isotopic variation in the atmosphere-crop-soil system by using natural abundance or tracer technique of stable carbon isotope contributes to revealing soil organic carbon decomposition, transformation and other dynamic processes. The carbon cycling processes and the related ¹³C isotopic fractionation were introduced. The theory and methods about the stable carbon isotope analysis and its applications in the research of soil carbon cycling of agricultural ecosystems were reviewed. Finally, comprehensive summations of the problem existing in current research in conjunction with the prospects of the future research on soil carbon cycling were proposed.