The pattern of raising duck in paddy field is a model in Chinese traditional agriculture. Which is a combination system of planting and breeding in rice paddy field in subtropical region. This model can increase the efficiency of using rice paddy field. Field experiments on N and P cycling from a rice- duck mutual ecosystems in double cropping rice region in Hunan Province were conducted from July to October in 2009, and a conventional rice field was used as control. This study applied Input-Output Analysis method to analyze N and P cycling in both rice-duck and conventional rice fields. The main objectives of this study were to provide theoretical and practical basis for further development and utilization of this classical agricultural technique. Neither chemical pesticides nor herbicides were applied throughout the growth period of rice in rice-duck mutual ecosystems, N fertilizer appliation was also reduced, and the surface water was maintained about 10 cm in depth during the period of raising ducks. Ducks of 50-day-old were introduced into the paddy field based on the holding capacity of 450 ducks per ha 17 days after seedling transplantation. These ducks were retrieved after the complete heading stage of rice in the experiments. The results showed that N and P outputs in conventional rice field were 127.76 and 62.02 kg/hm² respectively while the N and P outputs in the rice-duck mutual ecosystems were 153.50 and 59.03 kg/hm²,respectively. Raising ducks resulted in the increase of N outputs compared to the conventional rice field. Furthermore, N and P outputs from ducks were 23.98 and 3.10 kg/hm², respectively. Soil N and P occurred deficit in rice-duck mutual ecosystems. The N and P inputs from feeds were very high in the duck sub-system. In rice-duck mutual ecosystems, N and P input from chemical fertilizer were 72 kg/hm² and 13.10 kg/hm², respectively; N and P input from feed were 64.44 kg/hm² and 36 kg/hm², respectively; N and P input from duckling were 0.81 kg/hm² and 0.14kg/hm², respectively. During Late Rice growth season, duck growth increased feces N 14.27 kg/hm², feces P 16.10 kg/hm², and feces organic carbon was 157.54 kg/hm². Duck feces N and P cycling rate were 10.66% and 28.16% kg/hm², respectively.