Intermittent drainage can reduce methane (CH₄) emission from rice paddy soils, but nitrous oxide (N₂O) emission can increase. We believe that the slow released N fertilizer can mitigate N₂O emissions by reducing N lost to the environment. In this study, we tried to assess the influence of slow N fertilizer on effective greenhouse gas (GHG) reduction. We installed three different treatments, urea (U) treatment, controlled release fertilizer (CRF) treatment, and hairy vetch with urea (HV) treatment. The emission rates of CH₄ and N₂O were monitored using the closed chamber method during cropping and fallow season. The grain yield was investigated to calculate yield scaled greenhouse gas intensity (GHGI). Compared with U treatment, CH₄ emission was reduced in CRF but increased in HV treatment. In contrast, N₂O emission was increased in CRF but reduced in HV treatment. Grain yield was increased in CRF and HV treatment than U treatment. The GHGI was the lowest in CRF treatment by high grain yield and low GHG emission. In contrast, GHGI was the highest in HV treatment due to increased CH₄ emission. In conclusion, controlled release fertilizer can effectively reduce GHG emission. However, CRF application increased N₂O emissions during the fallow season, and further investigation is needed to determine whether this is due to the effect of fertilizer residues. In addition, due to field experiments that are easy to influenced by the environmental condition, it seems necessary to verify the research results through additional investigations over many years.