Irrigation regime and fertilizer nitrogen (N) are considered as the most effective agricultural management systems to mitigate greenhouse gas (GHG) emissions from crop fields, but few studies have involved saline–alkaline paddy soil. Gas emitted from saline–alkaline paddy fields (1-year-old and 57-year-old) was collected during rice growing seasons by the closed chamber method. Compared to continuous flooding irrigation, lower average CH4 flux (by 22.81% and 23.62%), but higher CO2 flux (by 24.84% and 32.39%) was observed from intermittent irrigation fields. No significant differences of N2O flux were detected. Application rates of N fertilizer were as follows: (1) No N (N0); (2) 60 kg ha−1 (N60); (3) 150 kg ha−1 (N150); and (4) 250 kg ha−1 (N250). The cumulative emissions of GHG and N fertilizer additions have positive correlation, and the largest emission was detected at the rate of 250 kg N ha−1 (N250). Global warming potential (GWP, CH4 + N2O + CO2) of the 57-year-old field under the N250 treatment was up to 4549 ± 296 g CO2-eq m−2, approximately 1.5-fold that of N0 (no N application). In summary, the results suggest that intermittent irrigation would be a better regime to weaken the combined GWP of CH4 and N2O, but N fertilizer contributed positively to the GWP.