Raising duck in paddy field is a traditional agricultural model in China. This model can increase the efficiency of using paddy field while rice plant is growing. Field experiments on C cycling from rice-duck mutual ecosystem were conducted from May to October in 2010 in the double cropping rice region in Hunan, and a conventional rice field was used as control. The Input-Output Analysis method was applied in this study to analyze C cycling in both rice-duck and conventional rice fields. Throughout the plant growing season, neither chemical pesticides nor herbicides were applied in rice-duck mutual ecosystems, and the surface water was maintained about 10 cm in depth during the period of raising ducks. Ducks of 22-day-old were introduced into the paddy field based on the holding capacity of 450 ducks per ha 24 days after seedling of early rice transplantation. Ducks of 30-day-old were introduced into the paddy field based on the holding capacity of 450 ducks per ha 10 days after seedling of late rice transplantation. These ducks were retrieved after the complete heading stage of rice in the experiments. During the early rice growth season, the recycled C from weed and insects in rice-duck mutual ecosystems were 60.53 kg/hm² and 2.75 kg/hm², respectively. The C inputs from urea, duckling, plant seedling and feed were 22.5 kg/hm²; 15.79 kg/hm²; 20.42 kg/hm² and 630.56 kg/hm², respectively. While the C outputs in the rice-duck mutual ecosystems consisted of 42.21% rice seed, 38.42% rice straws, 18.50%(CH₄ and CO₂)and 0.87% duck. During the late rice growth season, the recycled C from weed and insect in rice-duck mutual ecosystems were 3.64 kg/hm² and 6.73 kg/hm², respectively. The C inputs from urea, duckling, seedling and feed were 22.5 kg/hm²; 15.93 kg/hm²; 222.33 kg/hm² and 966.85 kg/hm², correspondingly. while the C outputs in rice-duck mutual ecosystems consisted of 53.80% rice seed, 35.12% rice straws, 8.67%(CH₄ and CO₂), 1.07% duck. Throughout the double cropping rice season, Soil C sequestration was 2103.2 kg/hm², and C sequestration by rice straws and rice seeds was 15109.96 kg/hm², by rice root was 1261.34 kg/hm². The feces C introduced by duck growth was 229.87 kg/hm². The C inputs from feeds were very high in the duck sub-system, which was 1597.41 kg/hm² during double cropping rice growth season. Analysis of C budget in double cropping rice-duck mutual ecosystems showed that rice-duck mutualism acted as a net CO₂ sink and possessed a better carbon storage potential.