[Objectives]  Transgenic Bt cotton has been widely cultivated in China. Decomposition of transgenic plant litter under different climate scenarios should be closely correlated with nutrient cycling and plant productivity. However, the interactive effect of transgenic cotton and elevated ozone on soil fauna has not been previously studied. [Methods]  A field litterbag experiment including two cotton varieties (GK12 and its control SM3) and two ozone concentrations (ambient air and elevated ozone) was designed to investigate the effects of transgenic cotton litter and ozone on soil Collembola in 2009. [Results]  Our results show that, both overall and in different cotton growth stages, density, species richness, diversity and community structure of Collembola in litterbags were not impacted by transgenic cotton varieties and elevated ozone concentration. Some groups such as Onychiurus spp.and Entomobrya spp. did, however, significantly decrease in transgenic cotton litterbags. This might have be caused by poor litter quality (higher cellulose and lignin content) in the transgenic cotton treatment. [Conclusion]  Litter decomposition of transgenic cotton and elevated ozone concentration did not have a significant effect on soil Collembola over the course of a one year experiment, however, some sensitive groups significantly decreased in the transgenic cotton litter treatment. Future experiments should focus on these sensitive groups.