Computational fluid dynamics (CFD) simulation provides full-field variables, enabling a better understanding of flow physics and associated heat transfer. However, assumptions involved in CFD simulation should not affect flow and temperature fields and their correspondence to practical situations. Therefore, the present study analyzed the importance of temperature-dependent fluid properties in a sealed container during thermal treatment. We compared the thermal behavior trends of temperature-dependent fluid properties with those obtained from constant properties for two carboxyl methyl cellulose (CMC) solution concentrations. The results show that natural convection occurs earlier in the temperature-dependent fluid properties, which leads to attaining a desired level of sterility within a shorter time than the constant properties of the fluid. The variations in the viscosity with the shear rate and temperature played essential roles in affecting thermal behavior. So, results indicate that temperature-dependent non-Newtonian fluid must be considered to avoid miscalculating heating time in conventional thermal treatment. Besides, the thermal trends of both cases approach pure conduction when CMC solutions’ apparent viscosity increases.