The warming potential of greenhouse gases such as N2O emitted by agricultural ecosystems was 265 times that of CO2, and the greenhouse effect it brings has a great impact on global warming and climate change. The use of controlled-release fertilizers (CRF) can reduce greenhouse gas emissions, but little was known about the mitigation effects and microbial mechanisms in the context of climate change. We investigated the effects of elevated CO2 concentrations (EC), elevated temperature (ET), and combined treatments of elevated CO2 concentration and elevated temperature (ECET) on N2O and CH4 emissions and related enzyme activities and gene abundances in winter wheat soils in climate-controlled open chambers. We found that the cumulative N2O emissions in the wheat-growing season ranged from 0.39 to 3.10 kg·ha-1. CRF reduced the cumulative N2O emissions. EC significantly affected the cumulative N2O emissions in the wheat-growing season in 2018-2019, while ET significantly affected the cumulative N2O emissions in the following year. There was no synergistic effect of the ECET with or without CRF. CRF can reduce N2O emissions by reduced nitrification and denitrification-related enzyme activities and gene abundances and regulating the ratio of N2O reduction and generation during the elongation stage. Under future climate change scenarios, CRF will reduce N2O emissions. But the greenhouse gas emissions under ECET treatment will be less than the sum of the individual effects.