The influence of transgenic Bacillus thuringiensis (Bt) cotton (BtXincai1) and its corresponding nontransgenic isoline (Xincai1) on the microorganisms, enzyme activity, and nutrient content of rhizosphere soil was studied through experiments in potted plants. The calcareous drab soil samples were collected (0–15 cm deep) from an experimental field in Shanxi Agricultural University (China) in 2005. The pots were categorized in different groups with replicates for each variety (transgenic BtXincai1 and general Xincai1). The rhizosphere soil samples were collected at different growth periods (seedling, bud, flowering, peak boll, boll opening, and harvest). The Bt protein and other microbial properties in the soil samples were determined by using selected methods (material and methods session). The results demonstrated that the concentration of the Bt protein in the rhizosphere soil of BtXincai1 reached a peak at 56.14 ng g&amp;#8722;1 during the flowering period. However, the Bt protein would not continuously accumulate in the soil. The rhizosphere soil of BtXincai1 was more suitable for the growth and proliferation of bacteria and fungi but it had no significant impact on the number of actinomycetes. BtXincai1 had some inhibitory effects on alkaline phosphatase activity in the rhizosphere soil, and it might promote dehydrogenase activity during the blooming period. However, it had no significant influence on protease, urease, or sucrase activities. Further, it had no significant impact on the contents of organic matter, total nitrogen, available nitrogen, or potassium in rhizosphere soil. It could significantly decrease the content of available phosphorus during the flowering period. Based on this study, the sensitive reactions of microorganisms and the activities of alkaline phosphatase and dehydrogenase might be considered as three potential indexes for assessing the risk posed by transgenic Bt cotton to soil ecology.