At present, research is lacking regarding the environmental behavior/fate of trinitrotoluene (TNT) pollutants produced by military activities and technologies for the efficient remediation of toxic byproducts. In this study, fresh explosive (TNT)-contaminated farmland soil was simulated to analyze the environmental behavior and trends of TNT using the enzyme system response, ionomers, microbial diversity, and the secondary nitrogen cycle network. Compound microbial agents were also prepared to repair soil contaminated by TNT, 2-amino-4,6-dinitrotoluene (2-ADNT), 4-amino-2,6-dinitrotoluene (4-ADNT), and 2,4-diamino-6-nitrotoluene (2,4-DANT). TNT significantly inhibited 23.1–63.6% of the soil nitrogen cycle-related enzymes. The soil ion network fluctuated significantly. The abundance of Sphingomonadaceae showing key tolerance/degradation TNT was significantly upregulated. Bryobacter and MND1 were important driving forces of soil community structure change. At the same time, TNT presence increased the risk of spread of soil biological diseases and unbalanced basic nucleotide, carbohydrate, and amino acid metabolism in the soil. The key network of the soil response to TNT was pyrimidine metabolism (biomarkers: uridine and deoxycytidine). Interestingly, soil glycolysis/gluconeogenesis and the tri carboxylic acid cycle (TCA cycle) maintained steady-state levels despite TNT toxicity. TNT was transformed into 17 soil metabolism intermediates. In addition, 12 isolated bacterial strains showed high degradation efficiency for TNT, 2-ADNT, 4-ADNT, and 2,4-DANT, and activated the mineral element defense network to resist the toxic effects of TNT, and Mn, Mg and B species were involved in the process of microbial degradation of pollutants. A compound mixture of these microbial agents efficiently degraded soil TNT and its intermediate toxic byproducts. Our analysis of the environmental behavior and trends for TNT provides a microbial remediation strategy for ammunition-contaminated soil and is of great significance for soil productivity recovery and climate change.