This study numerically investigates the effect of rheological liquid foods on heat sterilization process using Taylor–Couette flow sterilizer (TCFS). As model thermal processing, the destruction of Clostridium botulinum and thiamine was selected. It was found that the equivalent lethality slightly decreased with increase in the strength of shear-thinning property. On the other hand, there was no clear difference in the retaining performance of thiamine. Furthermore, the power consumption decreased with the increase in the strength of shear-thinning property. Thus, from the viewpoint of energy saving, it can be concluded that the utilization of TCFS to stronger shear-thinning food systems is more effective.