This study aims to mitigation greenhouse gas (GHG) emission and enhancing soil carbon sequestration in paddy rice field by comparing different agricultural practices (organic farming practice, good agricultural practice [GAP] and chemical farming practice) with water management in two cropping seasons for 1 year. Results from field investigation showed that organic practice had a high methane emission, due to organic fertilizer application. Reducing chemical fertilizer rate and fertilizer incorporating into soil in GAP reduced nitrous oxide emission, compared to chemical and organic practices. But, water drainage increased nitrous oxide emission for all the studied agricultural practices. Practices that can store soil carbon were in an order of organic > GAP > chemical fields, and the effect of practices were more pronounced than water management. Result from soil carbon budget was in agreement with the soil organic carbon (SOC) measured in the field. Organic field with 9 years conversion showed a higher SOC (>21%) than chemical fields. In addition, GAP field had a greater soil C storage than chemical field, due to higher rice residue biomass. Despite global warming potential (GWP) from soil C budget indicated that all studied agricultural practices caused a global warming, organic practice with water management (OW) and GAP could reduced GWP value to be lower or closer to chemical practice with water management (CW). Field observations suggested that OW practice could mitigate GHG emission and promoting soil carbon sequestration with no effect on rice yield, but reduced investment return. GAP had a slightly higher soil C sequestration than chemical farming, but was not much reduced GHG emission. CW practice reduced GHG emission, but had adverse effects on soil C storage, rice yield and investment return, which needed further investigation for better understanding. The DNDC model simulation showed that chemical practice with no water management (CC) provided the highest SOC and high rice yield, but resulted in highest GHG emission. In comparison with the CC practice, organic practice also had a high yield as chemical practice and reduced GHG emission by 2%, but slightly decreased SOC (0.06%). The water management effect was considerably observed in GAP with water management (GW) by decreasing SOC (0.4%) and rice yield, (0.7%) and enhancing GWPs (1.2%), when compared with GAP with no water management (GC). The results from model simulation agreed with field observation data and suggested organic rice production with water management is the best option for SOC stock in rice soil, remain high rice grain yield, and mitigate greenhouse gases emission. In addition, GAP rice production can be able apply as the second candidate for greenhouse gases mitigation with remain rice grain yield when compared to conventional rice production.