Taking non-transgenic parental rice as the control, and by using 13C pulse-chase labeling method coupled with phospholipid fatty acid (PLFA) analysis, this paper studied the effects of transgenic Bt rice on the microbial diversity in rhizosphere soil. The results showed that in the rhizosphere soils of transgenic Bt rice and its non-transgenic parent, saturated PLFAs and branched PLFAs were the main, followed by monounsaturated PLFAs, and polyunsaturated PLFAs. A significantly lower amount of Gram-positive bacterial PLFAs and a higher amount of Gram-negative bacterial PLFAs were observed in the rhizosphere soil of transgenic Bt rice at its seedling, booting, and heading stages, as compared with the control. In the whole growth period of rice, transgenic Bt gene had no significant effects on the fungal and actinomycete PLFAs in rhizosphere soil, and no significant difference was observed in the rhizosphere soil 13C-PLFA content between transgenic Bt rice and its non-transgenic parent. These findings indicated that the insertion of exogenous cry1Ab gene into rice only had temporary effects on the microbial community composition in the rhizosphere soil of rice.