In the FCC conversion of heavy petroleum fractions as atmospheric residues, the main challenge for refiners to achieve the quantity and quality of various commercial products depends essentially on the catalyst used in the process. A deep characterization of the catalyst at different steps of the process (fresh, regenerated, and spent catalyst) was investigated to study the catalyst’s behavior including the physicochemical evolution, the deactivation factor, and kinetic–thermodynamic parameters. All samples were characterized using various spectroscopy methods such as N2 adsorption–desorption, UV-visible spectroscopy, Raman spectroscopy, LECO carbon analysis, scanning electron microscopy (SEM), X-ray diffraction (XRD), X-ray fluorescence (XRF), nuclear magnetic resonance spectroscopy (NMR13C) analysis, and thermogravimetric analysis. The results of the N2 adsorption–desorption, UV-vis, Raman, LECO carbon, and SEM imaging showed that the main causes of catalyst deactivation and coking were the deposition of carbon species that covered the active sites and clogged the pores, and the attrition factor due to thermal conditions and poisonous metals. The XRD and XRF results showed the catalyst’s physicochemical evolution during the process and the different interlinks between catalyst and feedstock (Nickel, Vanadium, Sulfur, and Iron) elements which should be responsible for the coking and catalyst attrition factor. It has been found that, in addition to the temperature, the residence time of the catalyst in the process also influences catalyst structure transformation. NMR13C analysis revealed that polyaromatic hydrocarbon is the main component in the deposited coke of the spent catalyst. The pyridine-FTIR indicates that the catalyst thermal treatment has an influence on its Brønsted and Lewis acid sites and the distribution of the products. Thermogravimetric analysis showed that the order of catalyst mass loss was fresh > regenerated > spent catalyst due to the progressive losses of the hydroxyl bonds (OH) and the structure change along the catalyst thermal treatment. Moreover, the kinetic and thermodynamic parameters showed that all zones are non-spontaneous endothermic reactions.