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Determination of abdominal aortic aneurysm (AAA) rupture risk involves the accurate prediction of mechanical stresses acting on the arterial tissue, as well as the wall strength which has a correlation with oxygen supply within the aneurysmal wall. Our laboratory has previously reported the significance of an intraluminal thrombus (ILT) presence and morphology on localized oxygen deprivation by assuming a uniform consistency of ILT. The aim of this work is to investigate the effects of ILT structural composition on oxygen flow by adopting a multilayered porous framework and comparing a two-layer ILT model with one-layer models. Three-dimensional idealized and patient-specific AAA geometries are generated. Numerical simulations of coupled fluid flow and oxygen transport between blood, arterial wall, and ILT are performed, and spatial variations of oxygen concentrations within the AAA are obtained. A parametric study is conducted, and ILT permeability and oxygen diffusivity parameters are individually varied within a physiological range. A gradient of permeability is also defined to represent the heterogenous structure of ILT. Results for oxygen measures as well as filtration velocities are obtained, and it is found that the presence of any ILT reduces and redistributes the concentrations in the aortic wall markedly. Moreover, it is found that the integration of a porous ILT significantly affects the oxygen transport in AAA and the concentrations are linked to ILT’s permeability values. Regardless of the ILT stratification, maximum variation in wall oxygen concentrations is higher in models with lower permeability, while the concentrations are not sensitive to the value of the diffusion coefficient. Based on the observations, we infer that average one-layer parameters for ILT material characteristics can be used to reasonably estimate the wall oxygen concentrations in aneurysm models.