Understanding how soil ecosystem responds to transgenic Bacillus thuringiensis (Bt) rice is necessary for environmental risk assessment. While the influences of short-term cultivation of Bt rice on soil properties have been reported previously, little is known about the long-term effects of Bt rice on soil ecosystems. In this study, soil samples were taken from a long-term rice cultivation site in Fujian Province, China, where transgenic Bt rice (Kefeng-6) and its non-Bt parent breed (Minghui-86) had been continuously cultivated for 8 years. Soil Bt protein concentration and a total of 16 variables were analyzed to assess potential risks of soil health under Bt rice cultivation. The results revealed that soil Bt protein is unlikely to accumulate after Bt rice cultivated in the field, and no consistently significant changes were observed in soil enzymatic activities (catalase, dehydrogenase, acid phosphatase, and urease), microbial biomass (microbial carbon and nitrogen), total organic carbon, decomposition (soil respiration, Q 10, and qCO2), soil nitrogen and phosphorus contents. Due to a local tradition that aboveground biomass was removed after harvest, the increased net primary productivity by Bt rice cultivation did not significantly change soil C cycling. Results of this study suggested that on the aspects of soil microbial functioning and C cycling, long-term cultivation of Bt rice is unlikely to result in significant effects on soil health.