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In coastal saline rice fields, rice production shows high greenhouse gas (GHG) emissions but low nitrogen use efficiency (NUE). However, few studies have focused on the combined effects of nitrogen (N) fertilizer and soil ameliorants on GHG emissions. Thus, a field experiment was conducted to study the combined effects of N fertilizer, humic acid, and gypsum on the global warming potential (GWP), yield-scaled greenhouse gas intensity (GHGI), rice grain yield, and NUE in coastal saline rice fields in southeastern China. The experiment was conducted with eight treatments: N0, N1, N0H1, N1H1, N0G1, N1G1, N0H1G1, and N1H1G1. The codes N0, N1, H1, and G1 represented treatments without N (0 kg N ha(-1)), with N (300 kg N ha(-1)), with humic acid (0.6 t ha(-1)), and with gypsum (0.6 t ha(-1)), respectively. Compared with the treatments without N addition, the application of N fertilizer significantly increased N2O emissions and grain yield by 41.9 similar to 130.6% and 32.8 similar to 57.5%, respectively, while significantly decreased the yield-scaled GHGI by 9.4 similar to 31.9%. Humic acid amendment significantly increased N2O emissions and grain yield as compared with the treatments without humic acid. Gypsum addition had no significant effects on CH4 and N2O emissions, GWP, yield-scaled GHGI, and grain yield in relation to the treatments without gypsum. In addition, compared with the N1 treatment, the N1H1, N1G1, and N1H1G1 treatments increased the grain yield by 18.3% (p < 0.05), 2.3%, and 10.4%, and decreased yield-scaled GHGI by 9.6%, 20.5%, and 31.2% (p < 0.05), despite similar GWPs, respectively. Overall, the N1H1 and N1H1G1 treatments are the appropriate fertilizer management to realize high yield together with low environmental impacts in coastal saline rice fields in China.