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This study analyzed the effects of traditional rice cultivation (TC), ridge tillage and terrace rice cultivation (RC), and ridge tillage and terrace rice cultivation plus loach (Misgurnus anguillicaudatus) breeding in ditches (RLC) on methane (CH4) emissions and daytime net ecosystem production (NEP) of CO2 fluxes in a paddy ecosystem using the ultra-portable greenhouse gas (GHG) analyzer with a static transparent chamber. Rice plant characteristics and yields were also measured with field experiments and laboratory analysis. The aim was to explore the possible contribution of the rice ridge terraced cultivation to yield while reducing GHG emissions. We found that (1) RC has the highest rice yield for both the early-and late-season rice, followed by TC and RLC. (2) The combined CH4 emission and daytime NEP values were the least for RC during the double growing season, followed by TC and RLC. (3) Comparing the cumulative global warming potential and yield-scaled emission, RC showed the lowest GHG emission and the highest NEP for the double growing season, followed by TC and RLC. The results indicated that RC was beneficial for increasing rice yields while decreasing CO2 and CH4 emissions in the paddy ecosystem.