Nitrogen (N) fertilizer input will likely increase to meet the food demands of a growing population under climate change conditions, characterized by increasing atmospheric CO2 concentration and temperature. Nitrification inhibitors have the potential to reduce N2O emissions from N fertilized croplands. However, it remains unclear whether future climate change scenarios could affect the effectiveness of nitrification inhibitors. In a two-year study, winter wheat (Triticum aestivum L.) was cultivated in climate-controlled growth chambers with an elevated CO2 concentration (ambient +200 μmol mol−1) and increased temperature (ambient +2 °C). Urea was applied with or without nitrapyrin (0.5 % of urea-N). In this study, we measured nitrous oxide (N2O) fluxes, soil ammonium and nitrate levels, and the abundance of five nitrogen-cycling genes related to nitrification (amoA of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA)) and denitrification (nirS, nirK and nosZ). Key findings included the following: 1) without nitrapyrin, cumulative N2O emissions were not significantly altered by increased temperature, but decreased 24.9 % by the combination of elevated CO2 and temperature treatment and 17.5 % by the elevated CO2 alone. NO3−-N accumulation occurred in soils under increased CO2 and temperature, both individual and in combination; 2) nitrapyrin effectively reduced AOB abundance, inhibiting NO3−-N accumulation and N2O emission, irrespective of CO2 concentrations and temperature. However, under the combination of elevated CO2 and temperature conditions, the efficiency of nitrapyrin in reducing N2O emission was lower (−13 % to −49 %) than that in the control (−28 % to −65 %) and elevated CO2 (−32 % to −71 %) conditions. This reduced effectiveness of the combined treatment can be attributed to the inability of nitrapyrin to inhibit the AOA, nirS and nirK genes. Thus, nitrapyrin is expected to reduce N2O emissions under future climate change scenarios, but the efficacy may be lower than previously expected when CO2 concentration and temperature increase simultaneously. The indirect effects of nitrapyrin on denitrifiers under climate change scenarios should be considered in future research.