Aims <p>Transgenic <i>Bacillus thuringiensis</i> (<i>Bt</i>) crops are cultivated globally to mitigate potential pest crisis and reduce insecticide dependence. However, the response of belowground system to <i>Bt</i> crop cultivation remains controversial, limiting our understanding of <i>Bt</i> crops’ role in agriculture sustainability. The aim of this study was to assess <i>Bt</i> crops’ influence on soil system, including variables of soil respiration, soil carbon and nutrient pools, and soil biodiversity.</p> Methods <p>We conducted a global meta-analysis of 88 experimental studies to assess the influence of <i>Bt</i> crop cultivation on soil system.</p> Results <p>Alongside a 14.3% and 4.3% rise in above- and below-ground plant biomass, <i>Bt</i> crops also initiates a cascade of belowground ecological changes, including shifts in the stoichiometry of the crop-soil-microbe system and soil biodiversity, particularly the dominant increase in bacterial diversity over fungal diversity, which collectively accelerates the turnover of labile organic matter and stimulated soil respiration (+ 6.0%, <i>P</i> &lt; 0.05). The significant increase of microbial biomass carbon and its carbon: nitrogen ratio suggest that <i>Bt</i> crop cultivation may cause soil microbes to face a nitrogen limitation.</p> Conclusions <p>In contrast to traditional cropping systems, <i>Bt</i>-crop systems exhibit increased biomass accumulation along with elevated soil respiration, driven by shifts in systemic stoichiometry and biodiversity, which provides a compelling case for understanding Nash Equilibrium within ecosystems. <i>Bt</i> crops’ accelerating microbial nutrient mining and turnover of simple organic compounds in soil might suggest a necessity of synchronized fertilization, which would support the stability of rhizosphere environment and enhance the life-cycle carbon sink potential of transgenic crops.</p>