Abstract: The object of this study was to investigate carbon sequestration potential of rice-wheat rotation system in Jiangsu Province. The rice-wheat cropping fields along Yangtze River in Jiangsu province were chosen to estimate the carbon input, carbon output, carbon efficiency and economic income in rice and wheat production, based on research data of grain yield, material and labor inputs under different farming methods with full straw returning, including wheat-rice wide-row alternative protective farming technology mode and annual mechanized farming for rice and wheat. The results showed that the amount of annual carbon input under protective farming (PF) and mechanized farming(MF) were 1836.5 kg/hm2 and 2290.5 kg/hm2 respectively. Compared with MF, carbon input of seeds, chemical fertilizer and machinery under PF was lower, but carbon input of labor was higher. The annual carbon output under PF and MF were 18.23 t/hm2 and 16.15 t/hm2, respectively, and PF was 12.9% more than MF. The annual carbon efficiency also had significant difference between PF and MF. Compared with MF, PF increased production efficiency, ecological efficiency and economic efficiency of Carbon by 40.4%, 40.8% and 40.3%, respectively. Besides, the annual income net of PF reached 20.25×103 yuan/hm2 and was 22.8% more than MF. The results indicated that the protective faming method with full straw returning could increase carbon efficiency and economic income and realize a win-win situation of environment benefit and economic benefit.