In carbon anode baking furnaces, temperature and quality of carbon anodes are significantly affected by the deformation of the flue-walls, where the flue-gases flow and combustion occur. Flue-walls aging gives rise to non-homogeneous baking of the carbon anodes and results in deterioration of the anode quality, which eventually causes instabilities in aluminum reduction cells and overconsumption of anodes and energy. It is imperative to develop a fully coupled 3D multi-physics computational model which takes into account a large number of physical phenomena that play vital roles in the baking process and are affected by the flue-wall deformation mode. In the present study, the effects of flue-wall deformation modes on flue-wall cavity gas flow and anode temperature distribution are investigated. The pressure and flow distributions for different levels of flue-wall deformation are demonstrated. It is perceived that a 100 mm convex mode of flue-wall deformation leads to under-baking of anodes by almost 20 degC. For the concave mode of deformation, since the packing coke thickness reduces, overbaking of anode occurs. The methodology and results presented in the present research can be employed effectively by the aluminum industry in modifying the furnace geometrical and operational parameters to enhance baking uniformity after flue-wall is deformed.