Green manure application helps maintain soil fertility, reduce chemical fertilizer use, and carbon sequestration in the soil. Nevertheless, the application of organic matter in paddy fields induces CH4 and N2O emissions. Prolonging mid-season drainage reduces CH4 emissions in paddy fields. Therefore, the combined effects of green manure application and mid-season drainage prolongation on net greenhouse gas emission (NGHGE) were investigated. Four experimental treatments were set up over a 2-year period: conventional mid-season drainage with (CMG) and without (CM) green manure and prolonged (4 or 7 days) mid-season drainage with (PMG) and without (PM) green manure. Astragalus sinicus L. seeds were sown in autumn and incorporated before rice cultivation. No significant difference in annual CH4 and N2O emissions, heterotrophic respiration, and NGHGE between treatments were observed, indicating that green manure application and mid-season drainage prolongation did not influence NGHGE. CH4 flux decreased drastically in PM and PMG during mid-season drainage under the hot and dry weather conditions. However, increasing applied carbon increases NGHGE because of increased CH4 and Rh. Consequently, combination practice of mid-season drainage prolongation and green manure utilization can be acceptable without changing NGHGE while maintaining grain yield in rice paddy fields under organically managed rice paddy fields.