To investigate the effects of nitrification inhibitors applied in the wheat season on the soil inorganic nitrogen (N), N2O emissions and related enzyme activities in the soybean season for the wheat-soybean rotation system under the background of climate change, different atmospheric CO2 concentration (400 and 600 μmol/mol) and air temperature (ambient temperature T and T+2℃) were set in the control air chamber. The contents of soybean soil nitrate and ammonium N, nitrification and denitrification-related enzyme activities and N2O emissions were measured when nitrification inhibitors were added in the wheat season. The results showed that the addition of nitrification inhibitor combined with wheat straw returning to the field in wheat season increased soil nitrate N and ammonium N in soybean season, whereas it had little effect on the enzyme activities of soil nitrification-denitrification. Elevated air temperature (ET) significantly increased the content of nitrate N in soybean soil, while the content of ammonium N significantly decreased. At the conditions of increased atmospheric CO2 concentration (EC) or simultaneously increased air temperature and CO2 concentration (ECT), soil nitrate N and ammonium N content both increased, whereas there were no significantly difference with the inorganic N content under ambient temperature and CO2 concentration (CK). The enzyme activities of soil nitrification-denitrification under different environmental conditions showed no obvious regularity. Under ET and ECT conditions, the total amount of N2O emission in soybean growing season was significantly higher than that in CK treatment, and the addition of nitrification inhibitors reduced N2O emission. The difference of N2O emissions between EC and CK conditions was small, whereas the N2O emission of nitrification inhibitor treatment was significantly higher than that of common urea treatment under CK condition. To sum up, under the background of rising air temperature and CO2 concentration in the future, reasonable application of nitrification inhibitors is beneficial to the increase of available N in soybean soil, whereas the increase of air temperature (ET and ECT) may increase N2O emissions, and adding nitrification inhibitors can reduce N2O emissions. The changes in N2O emissions are not obvious when the CO2 concentration (EC) increased alone. This study can provide a theoretical support for fertilization management and farmland N2O emission reduction under the wheat-soybean crop rotation system under the background of future climate change.