To estimate greenhouse gas (GHG) emission, the inventory of rice cultivation at the farming without agricultural chemicals was established from farmers in Gunsan, Jeonbuk province in 2011~2012. The objectives of this study were to calculate carbon footprint and analyse the major factor of GHGs. To do this, we carried out a sensitivity analysis using the analyzed main factors of GHGs and estimated the mitigation potential of GHGs. Also we suggested agricultural methods to reduce GHGs that can be appled by farmers at this region. At the farming system without agricultural chemicals, carbon footprint of rice production unit of 1 kg was 2.15 kg $CO_2.-eq.kg^{-1}$. Although the amount of carbon dioxide ($CO_2$) emission was the largest among GHGs, methane ($CH_4$) emission had the highest contribution to carbon footprint on rice production system when it was converted to carbon dioxide equivalent ($CO_2-eq.$) multiplied by the global warming potential (GWP). Main source of $CO_2$ emission in the rice farming system without agricultural chemicals was combustion of fossil fuels used by agricultural machinery. Most of the $CH_4$ was emitted during rice cultivation practice and its major emission factor was flooded paddy field in anaerobic condition. Also, most of the $N_2O$ was emitted from rice cultivation process. Major sources of the $N_2O$ emission was application of fertilizer such as compound fertilizer. As a result of sensitivity analysis in energy consumption, diesel had the highest sensitivity among the energy inputs. With the reduction of diesel consumption by 10%, it was estimated that $CO_2$ potential reduction was about 2.0%. With reducing application rate of compound fertilizer by 10%, the potential reduction was calculated that $CO_2$ and $N_2O$ could be reduced by 0.5% and 0.9%, respectively. At the condition of 10% reduction of silicate and compost, $CO_2$ and $CH_4$ could be reduced by 1.5% and 1.6%, respectively. With 8 days more drainage than the ordinary practice, $CH_4$ emission could be reduced by about 4.5%. Drainage and diesel consumption were the main sources having the largest effect on the GHG reduction at the farming system without agricultural chemicals. Based on the above results, we suggest that no-tillage and midsummer drainage could be a method to decrease GHG emissions from rice production system.