The emission pattern of greenhouse gas (GHG) has been intensively investigated in different agro-ecosystems, but the underlying microbial mechanism in soil is still poorly understood, especially under many possible measures for improving nitrogen utilization. Thus, a 28-day laboratory microcosm experiment was conducted with an upland soil to investigate the effect of urea and two nitrification inhibitors on nitrogen turnover process and global warming potentials (GWP) of N₂O, CO₂ and CH₄, in which four treatments were established: CK (no fertilizer and inhibitor were applied), Urea (N 100 μg/g was applied to soil), Urea+15% Dicyandiamide (DCD, 15% of Urea-N in quantity), Urea+5% Allylthiourea (ATU, 5% of Urea-N in quantity). Meanwhile, the dynamics of different microbial abundances in treatments were also quantified by real-time quantitative PCR (qPCR). The results showed that ammonia-oxidizing bacteria (AOB) predominated intensive nitrification process and N₂O emission in soil with urea application. Urea stimulated AOB growth and increased cumulative N₂O by 235%, which rapidly occurred during the first 14 days. Bactria abundance raised in response to urea and improved CO₂ emission by 18.5%. Urea+DCD severely inhibited AOB and decreased N₂O emission by 59.4%, but stimulated bacteria and increased CO₂ by 50.6%. Urea+ATU exhibited a strong toxicity on both bacteria and fungi and led to a decrease of CO₂ by 28.4%, but unexpectedly didn't show any inhibition on nitrification intensity. A slight but significant inhibition and stimulation were observed on AOB and denitrifiers by ATU, respectively, but total emission of N₂O fell by 35.2%. CH₄ emission was inhibited in all treatments with urea and inhibitors. GWPs of N₂O, CO₂ and CH₄ displayed significant differences among treatments: Urea+DCD>Urea>CK>Urea+ATU. The contributions of N₂O and CO₂ to GWP exceeded 98.4% in soil. This study implies various mechanisms of nitrification inhibitors on soil microbial guilds and GHG emission, and is essential for the implementation of agricultural management and the evaluation of global climate change.