The development of a mathematical model for a process is reaching assumptions regarding the way the process can be accomplished. Fermentation is an exothermic reaction that causes an increase in the temperature of fermentation environment. Therefore, the present study tries offering an appropriate model for temperature changes of the sugarcane molasses fermentation environment. To thermally model the fermentation process, Fourier heat conduction equations have been utilized. A cylindrical reactor was used to perform the fermentation process; so, Fourier’s heat conduction equation was investigated and evaluated in 2D to model heat conduction and investigate the heat distribution trends in fermentation environment following which the 2D model was solved based on finite element method. To do so, heat conduction was once investigated in xy-direction and once in yz-direction using the same equation. To model the heat conduction along xy-direction, the problem domain considered herein was circular and also the circle quarter was employed for modeling due to the axial symmetry of the circle and parallel to reducing the number of calculations. The domain (quadrant) was divided into 6-nod triangular elements following which the model’s geometrical shape was drawn in the form of a quadrant with 466 elements and 1062 nods. The modeling of the temperature changes during the fermentation process and investigation of the temperature distribution in reactor shows that the fermentation environment temperature increases by 10°C to 15°C as a result of microorganisms and this has also been confirmed by the other researchers.