Controlled-release nitrogen fertilizers (CRF) are widely used in agricultural production to reduce conventional fertilization-induced agricultural greenhouse gas emissions. However, the long-term effects and associated mechanisms remain unclear. Therefore, this study investigated variations in agricultural greenhouse gas emissions at different growth stages under treatments of zeolite with CRF based on a 5-year field experiment. Results showed that both annual and yearly cumulative N ₂O and CO ₂ emissions were significantly reduced across all the three treatments relative to control. The treatment of nitrification inhibitor-controlled release N fertilizer with zeolite (T4) performed the best, followed by CRF (T3). Both the peak N ₂O and CO ₂ emissions occurred at the lotus stage. The crop nitrogen content of control was reduced by 12.5%, while the nitrogen content of other treatments was reduced by 5.90% to 11.4%. The T4 treatment delayed the oxidation of NH ₄ ⁺ and reduced CO ₂ emissions. The N ₂O and CO ₂ emission reductions significantly descended and then the decrement narrowed with the planting years increasing. Therefore, using blended controlled-release N fertilizer with zeolite to reduce chemical N application is a practically and environmentally friendly approach for greenhouse gases emissions reduction in the lettuce rotation system.