An incubation experiment was conducted to study the effects of the urease inhibitors N-butyl-thiophosphate triamide (NBPT) and Phenyl-phosphoryl-diamine (PPD) on soil intracellular/extracellular urease activities and bacterial, fungal, and archaea gene (conventional gene and ureC) abundances and their relationships. Urease inhibitors significantly decreased soil extracellular urease while significantly increasing soil intracellular urease activity, and NBPT was more effective in this regard than PPD. During the incubation period, the urease inhibitors significantly increased bacterial 16S rRNA and fungal ITS abundances but had no significant effect on archaea 16S rRNA abundance. The urease inhibitors also significantly increased bacterial ureC abundance and affected the ureC abundance of fungi to varying degrees. A Pearson correlation analysis showed that bacterial 16S rRNA abundance was significantly positively correlated with bacterial ureC abundance, which also suggested a closer relationship between intracellular urease and bacterial gene abundances than between those of fungi and archaea. Our results suggest that after the addition of urease inhibitors decreased extracellular urease activity and had a positive feedback effect on soil microbes, leading to significantly increased abundances of microbial genes, especially ureC, and resulting in increased intracellular urease reserves. Bacteria play a more important role than fungi and archaea in this process.