The carbon anode baking is typically the bottleneck in the production of anodes for the aluminum industry. The challenge is to produce high quality baked anodes while keeping the energy consumption, environmental emissions, and cost to a minimum. Anode baking homogeneity is an important consideration in the design and operation of the anode baking furnaces. The flue-walls, into which the firing takes place, are the heart of the furnace. The flue-walls must be well designed and well maintained in order to be able to regulate them properly. However, during the service life of a baking furnace, flue-walls deform which affect the baking uniformity and consequently result in over-consumption energy and reduction in carbon anode quality. Studying the effects of flue-wall deformation by plant tests is highly challenging and expensive. Hence, this study aims at investigating this phenomenon by developing a three-dimensional (3D) model which includes many physical phenomena and parameters that play vital roles in the baking process. It was observed that indeed the flue-wall deflection has a significant impact on heat transfer characteristics of the anode baking process and furnace energy consumption. In specific, the flue-wall deformation results in an increase in temperature gradients within the anode pack such that the differences between anode pack minimum, average and maximum temperatures lead to overbaking or underbaking of anodes. In fact, this non-uniform baking gives rise to the evolution of non-homogeneous carbon anodes material properties, which is the main reason for excess energy consumption and various instabilities in the aluminum reduction cell. The insights obtained in the present study can be employed in modifying the furnace geometrical and operational parameters with the deformed flue-walls.