Fe-rich intermetallics, especially β-Fe phase, usually forming in the microstructure of cast aluminum alloys, are very detrimental to mechanical properties. In the present work, the effects of Fe content on phase transformation and microstructures were analyzed using a 3D X-ray microscope. Based on the high-resolution 3D X-ray computed tomography, the 3D characteristics of Fe-rich intermetallics and micropores in the gravity-cast Al-6Si alloys with different Fe contents were investigated. In addition, the effect of intermetallics on the microporosity was discussed. The results show that with increasing the Fe content from 0.10wt.% to 0.60wt.%, the volume fraction of Fe-rich intermetallics and the volume of the largest size Fe-rich intermetallic increased, and the 3D morphology of intermetallics changed from fine flake to network aggregation. As the Fe contents increased, the shrinkage pores were characterized, which were rather complex due to the micropores promoted by the intermetallics interactions.