Alternative irrigation between saline water and groundwater can alleviate shortages of available agricultural water while effectively slowing the adverse effects of saline water on the soil-crop system when compared with continuous irrigation with saline water and blending irrigation between saline water and groundwater. In 2018, we tested the effect on soil CO2 and N2O emissions by two types of irrigation regimes (alternating groundwater and saline water (GW-SW), and alternating groundwater, followed by two cycles of saline water (GW-SW-SW)) between groundwater and three levels of salinity of irrigation water (mineralization of 2 g/L, 3.5 g/L, and 5 g/L), analyzed the correlation between gas emissions and soil properties, calculated comprehensive global warming potential (GWP), and investigated the maize yield. The results show that, with the same alternate irrigation regime, cumulative CO2 emissions decreased with increasing irrigation water salinity, and cumulative N2O emissions increased. Cumulative CO2 emissions were higher in the GW-SW regime for the same irrigation water salinity, and cumulative N2O emissions were higher in the GW-SW-SW regime. The GW-SW-SW regime had less comprehensive GWP and maize yield as compared to the GW-SW regime. The 2 g/L salinity in both regimes showed larger comprehensive GWP and maize yield. The 3.5 g/L salinity under the GW-SW regime will be the best choice while considering that the smaller comprehensive GWP and the larger maize yield are appropriate for agricultural implication. Fertilizer type and irrigation amount can be taken into consideration in future research direction.