The segregation behavior of a rheological high pressure die-casting (Rheo-HPDC) AC46000 aluminum alloy at positions with different wall thicknesses was studied. The results reveal that positions with different wall thicknesses exhibit different cooling rates that can result in distinctly different segregation characteristics. Segregation results in varying microstructure, elemental distribution, and hardness along the thickness of an alloy. The segregation in a Rheo-HPDC AC46000 alloy can be categorized as: cross-sectional segregation along the thickness and center segregation. As the distance from the alloy surface increases, the volume fraction of the primary phase increases, and the hardness of the microstructure and content of the eutectic Al-Si, Al2Cu, and α-(FeMn)3Si2Al15 phases decrease. As the alloy wall thickness increases, the differences in the volume fraction of the primary phase, elemental content, and hardness of the microstructure between the edge and center gradually decrease. Compared with the normal center microstructure, the volume fraction of the primary phase in the center segregation microstructure is lower, and the morphology is not round. The content of the eutectic Al-Si, Al2Cu, α-(FeMn)3Si2Al15, and Si phases is higher, and these phases are nonuniformly distributed. Center segregation is often accompanied by shrinkage cracks. As the alloy wall thickness increases, the center segregation area and crack size increase, and the more hard–brittle α-(FeMn)3Si2Al15 particles accumulate the crack. The hardness of the center segregation structure is higher than that of the normal center structure. With increasing alloy wall thickness, the hardness of the center segregation microstructure first increases and then decreases.