In this study, effects of transgenic Bt cotton on the structure, composition, and biodiversity of arthropod communities were systematically investigated in cotton fields over five consecutive years, from 2009 to 2013. Non-transgenic cotton ‘CCRI 49’ was used as the control, and transgenic Bt cotton ‘CCRI 41’ was used as the test material. Effects of transgenic Bt cotton on arthropod communities provide an important theoretical basis for the comprehensive management of cotton insect pests and ecological control, as well as a scientific reference for the evaluation of the environmental safety of transgenic Bt cotton. In addition, sustainable development and use, which are in accordance with ecological succession, can be adopted on the basis of production and need for pest control in cotton plants. In this study, arthropod communities were systematically investigated in transgenic Bt cotton ‘CCRI 41’ and conventional cotton ‘CCRI 49’ fields, from 2009 to 2013. In addition, meteorological factors during these five consecutive years were considered when analyzing the changing trends of relevant factors in the cotton field arthropod communities. The results showed that, during 2009-2013, the number of "orders" in the insect community, pest sub-community, and natural enemy sub-community in the "CCRI 41" cotton fields increased in comparison with the control cotton fields, but the differences were not significant. The number of "families," "species," and "total number of individuals" showed an increasing trend over the first 3 years and then declined in the last 2 years (2012 and 2013). The differences were significant in some years, which might be due to the meteorological conditions, while fluctuations were within statistical limits in other years. The diversity indices of the insect and pest sub-communities showed declining trends, which were statistically significant in 2013 but not significant in the other years. There was no significant change in the diversity index of the natural enemy sub-community. In addition, there was no significant change in the uniformity indices of the insect, pest, and natural enemy sub-communities. The dominant concentration indices of the insect and pest sub-communities increased over the 5-year period, but the increase was only significant in 2013. There was no significant change in the dominant concentration index of the natural enemy sub-community in 2009-2013.There were no significant changes in the structure or composition of the cotton field insect, pest, or natural enemy sub-communities in Bt cotton ‘CCRI 41’ fields, nor were there any changes in the diversity, uniformity, or dominant concentration indices. It can be inferred from the results that there were no significant changes in the structure, composition, and biodiversity of the arthropod, pest, and natural enemy sub-communities in Bt cotton fields during the planting period. However, this study was a short-term comparative investigation of only one pair of cotton varieties. The long-term effects of planting transgenic Bt cotton on the structure, composition, and biological diversity of arthropod communities need to be investigated and monitored in the future. This will provide scientific data for a long-term safety risk assessment of transgenic Bt cotton.