Nitrous oxide (N2O) is a greenhouse gas primarily released by fertilizers used in crop cultivation. In Thailand, cropland occupies the majority of the arable land but studies on N2O emissions from cropland remain scarce. The present study aimed to evaluate the N2O emissions, soil characteristics, and crop productivity resulting from different long-term fertilizer applications in a crop rotation of maize and mung bean. A long-term experimental field managed through crop residue incorporation combined with different fertilizer applications over 45 years was utilized in this study. It consisted of four distinct treatments: no fertilizer (CON), 134 kg N ha−1 from organic fertilizer (ORG), 188 kg N ha−1 from chemical fertilizer (CHE), and 322 kg N ha−1 from a combination of organic and chemical fertilizers (OAC). Long-term application of chemical fertilizer induced soil acidification, whereas the use of organic fertilizer maintained soil pH and enhanced soil carbon accumulation. Results showed that the OAC, CHE, and ORG practices significantly (p < 0.05) increased direct N2O emissions from the soil, particularly during the maize cultivation period. Annual cumulative N2O emissions were enhanced on average by 204 % (3.22 kg N2O ha−1) in OAC, 181 % (2.98 kg N2O ha−1) in CHE, and 79.4 % (1.90 kg N2O ha−1) in ORG compared with CON (1.06 kg N2O ha−1), indicating that larger N input rates induced larger N2O emissions. Chemical fertilizer induced significantly (p < 0.05) larger and faster N2O emissions than organic fertilizer. When considering N2O emissions per N application rate in all treatments as the emission factor, the use of N fertilizers combined with crop residues in the soil over two years averaged 0.61 % (± 0.13 %). This value was approximately 39 % lower than the default value recommended by the Intergovernmental Panel on Climate Change, which is currently used in Thailand. The consecutive addition of fertilizers significantly (p < 0.05) increased maize grain yield compared with the CON. However, no significant differences were observed among the various fertilizer treatments. Despite all fertilizer applications induced larger N2O emissions, they also produced greater crop yields. Consequently, this study recommended the practice of ORG as a means to mitigate emissions without compromising crop yield and soil quality.