[Objective] The soil microbial communities and N2O emissions were compared between soil samples from a vegetable greenhouse and outside farmland. [Methods] Denaturing gradient gel electrophoresis (DGGE) and quantitative PCR were used to investigate the difference of soil microbial communities and functional gene abundance, respectively. A robotized incubation system was employed to analyze the gaseous products of denitrification and calculate the ratio of N2O/(N2+N2O+NO). [Results] Significant differences were observed in soil bacterial communities between the two soils. The total number of bacteria in the greenhouse soil was higher than that of farmland. However, relative abundance of functional genes (nirS and nosZ) of the two types of soil was no significant difference. There were lower N2O accumulation and N2O/(N2+N2O+NO) ratio in the farmland soil compared to the greenhouse soil. In addition, the patterns of gas emissions in the two soils were significantly different in the early stage of anaerobic incubation. DNRA might lead to the increase of ammonium nitrogen content after the anaerobic incubation. [Conclusion] The higher strength of fertilization in greenhouse soil resulted in significant changes in soil bacterial communities and higher active soil microbial mass, N2O accumulation and N2O/(N2+N2O+NO) ratio. The soils from a greenhouse and a farmland, of which the greenhouse soil came from, have distinct nitrate respiration property. DNRA may be responsible for certain amounts of N2O emissions in both soils.