SummarySoil transplant into warmer regions has been shown to alter soil microbiology. In contrast, little is known about the effects of soil transplant into colder regions, albeit that climate cooling has solicited attention in recent years. To address this question, we transplanted bare fallow soil over large transects from southernChina (subtropical climate zone) to central (warm temperate climate zone) and northernChina (cold temperate climate zone). After an adaptation period of 4 years, soil nitrogen components, microbial biomass and community structures were altered. However, the effects of soil transplant on microbial communities were dampened by maize cropping, unveiling a negative interaction between cropping and transplant. Further statistical analyses with Canonical correspondence analysis and Mantel tests unveiled annual average temperature, relative humidity, aboveground biomass, soilpHandNH4+‐Ncontent as environmental attributes closely correlated with microbial functional structures. In addition, average abundances ofamoA‐AOA(ammonia‐oxidizing archaea) andamoA‐AOB(ammonia‐oxidizing bacteria) genes were significantly (P < 0.05) correlated with soil nitrification capacity, hence bothAOAandAOBcontributed to the soil functional process of nitrification. These results suggested that the soil nitrogen cycle was intimately linked with microbial community structure, and both were subjected to disturbance by soil transplant to colder regions and plant cropping.