In temperate rice paddy fields, winter cover cropping and its biomass application are strongly recommended to increase soil organic carbon (SOC) stock and decrease global warming potential (GWP). However, its biomass application may increase greenhouse gas (GHG) emissions, particularly methane (CH4), during flooded rice cultivation. To evaluate the effect of cover cropping and its biomass application on the annual net GWP in a mono-rice cultivation system, we evaluated the emission rates of CH4, nitrous oxide (N2O), and carbon dioxide (CO2) under different cover cropping during the fallow and rice-growing seasons. In cover cropping treatments, barley, hairy vetch, and a barley and hairy vetch mixture were cultivated as winter cover crops without fertilization during the fallow season. Moreover, the total aboveground biomass was incorporated as a green manure one week before rice transplanting. The recommended levels of chemical fertilizers were applied for rice cultivation in the control treatment (NPK) for comparison. The emission rates of CH4, soil respiration, and N2O gases were simultaneously monitored once a week using the closed-chamber method. However, the soil respiration fluxes included only soil respiration and excluded soil C sequestration through cover cropping and its biomass recycling. The net ecosystem C budget (NECB), which is defined as the difference between the total organic C input and output, was estimated to ascertain the pure soil respiration emission fluxes by mass balance approach. Finally, the net GWP was compared among treatments for the two cultivation seasons. During the dry fallow season, cover cropping significantly increased the soil respiration, and this treatment mineralized C loss significantly increased the seasonal net GWP. In comparison, the cover crop biomass application as green manure increased the soil C balance (NECB) during the rice growing season but more significantly increased the CH4 emission. As a result, the cover cultivation and its biomass application greatly increased the annual net GWP scale upon cover cropping rice paddy soil. Therefore, soil management practices that can decrease CH4 emission during rice cultivation should be adopted in cover cropping of the rice paddy soil.