Soil protease plays a fundamental role in soil nitrogen (N) transformations. Soil N and phosphorus (P) management significantly influence soil protease activity. However, the impacts of N and P combined modification on soil protease remain unclear. A better understanding of the activity and dynamic of soil protease could provide new insights into soil N cycling and available N supply. This study aimed to quantify the influences of combined effects of N and P managements on soil protease activities and decipher the potential mechanism from the perspectives of soil chemical properties, functional microbes, and functional genes. The nitrification inhibitor 3, 4-dimethylpyrazole phosphate (DMPP) application or phosphate-solubilizing bacteria (PSB) Klebsiella inoculation significantly increased soil protease activity (23.39% and 70.99%, respectively) and ammonium N (NH4+–N) contents, relative to the blank control. However, compared with the DMPP or PSB alone application, the combined applications of DMPP and PSB significantly decreased protease activity, implying that an antagonistic effect on soil protease activity was generated. The abundances of genus Klebsiella were stimulated by the DMPP or PSB but significantly inhibited by the combined additions of DMPP and PSB. The DMPP and PSB applications also significantly changed soil microbial communities and led to more complicated soil microbial co-occurrence networks. Soil protease activity had a significantly positive correlation with the normalized abundances of tri and clpX genes. Our findings suggested that the combined additions of DMPP and PSB generated an antagonistic effect on soil protease activity and that the antagonistic effect was directly associated with soil NH4+–N and NO3−–N contents, P fractions, and functional gene abundances.