This paper presents a non-isothermal, non-Newtonian Computational Fluid Dynamics (CFD) model for the mixing of a highly viscous polymer suspension in a partially filled sigma blade mixer. The model accounts for viscous heating and the free surface of the suspension. The rheological model is found by calibration with experimental temperature measurements. Subsequently, the model is exploited to study the effect of applying heat both before and during mixing on the suspension’s mixing quality. Two mixing indexes are used to evaluate the mixing condition, namely, the Ica Manas-Zlaczower dispersive index and Kramer’s distributive index. Some fluctuations are observed in the predictions of the dispersive mixing index, which could be associated with the free surface of the suspension, thus indicating that this index might not be ideal for partially filled mixers. The Kramer index results are stable and indicate that the particles in the suspension can be well distributed. Interestingly, the results highlight that the speed at which the suspension becomes well distributed is almost independent of applying heat both before and during the process.