Abstract: The diversity of soil microbial community and utilization pattern of polymer, amine, amino acid, carbohydrate, carboxylic acid and miscellaneous carbons were assessed via Biolog method on the 10th, 25th, 40th, 55th and 70th day of transgenic Bt cotton ground leaves decomposition. The results show decrease in soil microbial community richness and diversity, and increase in concentration index with ground leaves of transgenic Bt cotton. Ground leaves of transgenic Bt cotton has no effect on polymer and miscellaneous carbon utilization by soil microbes. It, however, obviously improves amine, amino acid and carbohydrate carbon utilization and also significantly debases carboxylic acid carbon utilization at the early stage of decomposition. Principal component analysis indicates that transgenic Bt cotton ground leaves have a sustained influence on indigenous soil microbial community structure and function.