Abstract The feedback of greenhouse gas emissions to climate change is vital for understanding and predicting the impact of global warming on ecosystem functions. However, the legacy effect of simulated climate change on nitrous oxide (N2O) emissions and the associated microbial guilds remain largely unknown. Using a climate change field-based mesocosm facility, we studied the impact of a warmer and drier environment and its legacy effect on in situ N2O emissions with different fertilizer types (manure and urea). The related functional guilds including N2O-producer [ammonia-oxidizing archaea and bacteria (AOA and AOB), nirS/K-type denitrifying bacteria, and nirK-type denitrifying fungi] and N2O-reducer (nosZI and nosZII) were analyzed by using high throughput and cloning sequencing. The simulated climate change significantly decreased in situ N2O emissions in the fertilized soil (urea- or manure-treated) while increasing the emissions in a non-fertilized soil. The AOA and AOB were well adapted to the simulated climate change condition in the manure- and urea-treated soil, respectively. In contrast, the fungal nirK-type N2O-producers were well adapted in non-fertilized soil. The abundance of nosZII was significantly stimulated by simulated climate change in both fertilized and non-fertilized soils. Moreover, different fertilizer types modulated the resilience of the microbial guilds. The AOA and the nirS-type denitrifying bacteria showed strong resilience, leading to a significant increase of N2O emissions in the manure-treated soil. The strong resilience was also observed in nosZII clade N2O-reducers, and the abundance of the species related to Candidatus Promineofilum breve and Gemmatirosa kalamazoonesis was stimulated by the legacy effect of simulated climate change in the urea-treated soil. The in situ N2O emissions were negatively correlated to nosZII rather than nosZI. These results highlight a significant potential of nosZII in mitigating N2O emissions under a projected climate change, especially in agroecosystems, where a large amount of fertilizers is commonly used.