Preventing soil biological degradation under the cultivation of Bacillus thuringiensis (Bt) crops is crucial to soil health. Despite studies concerning environmental risks of Bt crops, we surprisingly know little about whether soil biological degradation occurs under Bt crop cultivations. To fill this gap, we calculated the index of resistance (IR) and resilience (IR′) of 13 soil properties (the activities of enzymes, the rates of ecosystem processes, soil microbial biomass, and soil carbon and nutrients) using soil samples collected from an 8-year Bt rice cultivation experiment, including three treatments, that is, continual cultivation of Bt rice (GM) and non-Bt rice (non-GM), and rotation between Bt and non-Bt rice every 2 years (GM/non-GM rotation). In GM and GM/non-GM rotation, the IR of the activities of dehydrogenase, acid phosphatase, methane production rates was significantly greater than that in non-GM. Further, the IR of denitrification, methane oxidation, microbial carbon, and microbial nitrogen was significantly lowered in GM, and the IR of microbial carbon in GM/non-GM rotation was significantly decreased compared with that in non-GM. However, the results of IR′ showed no significant differences in these soil properties between treatments, except for methane oxidation and urease in GM and microbial nitrogen in GM/non-GM rotation. Taking into consideration of soil resistance and resilience, the most soil properties remained relatively stable. These findings suggest that the Bt rice cultivations have not significantly resulted in soil biological degradation.