The performance of the Taylor-Couette flow apparatus as a heat sterilizer is numerically investigated. The destruction of Clostridium botulinum and thiamine (vitamin B1) was selected as model reaction. When Taylor vortices were formed in the annular space, the heat transfer significantly enhanced as compared to the case without vortex flow. As a result, the equivalent lethality calculated from the temperature field increased, which is regarded as a quantum leap. Conversely, the improvement of heat transfer induced destruction of thiamine. These results suggest that there is a trade-off relationship between the enhancement of heat transfer and the avoidance of thermal destruction of nutritional components. In conclusion, the Taylor-Couette flow sterilizer has the potential for process intensification in heat sterilization processes.