A high Fe content easily produces Fe-rich phases with a harmful morphology, resulting in a huge detrimental effect on the properties and recycling ability of Al-Si alloys. Therefore, finding ways to effectively transform Fe-rich phases to form a beneficial phase or shape is of great significance. Accordingly, Al-Si-based alloys with Fe contents ranging from 0.1 wt.% to 2.0 wt.% were modified by different Mn additions. Moreover, experiments combined with simulations were utilized to comprehensively analyze the mechanism of Mn on the morphology and microstructural evolution of Fe-rich phases from different perspectives. The current findings determine that adding different Fe contents changes the phase-transition reactions in alloys. Without Mn, and by increasing the Fe content from 0.1 wt.% to 2.0 wt.%, the Fe-rich phases gradually convert from a skeleton-shaped α-Al8Fe2Si (<0.25 wt.%) to β-Al9Fe2Si2 with a fibrous (0.5 wt.%), needle-like (1.0 wt.%) and plate-like shape without curvatures (2.0 wt.%). The maximum length and mean aspect ratio increase from 12.01 μm to 655.66 μm and from 1.96 to 84.05, while the mean curvature decreases from 8.66 × 10−2 μm−1 to 8.25 × 10−4 μm−1. The addition of 0.35 wt.% Mn promotes a new Chinese-character and petal-shaped α-Al15(FeMn)3Si2, with an atomic ratio of Fe and Mn of 1:1 when the Fe content is lower than 0.5 wt.%, while it transforms to β-Al15(FeMn)3Si2 with an atomic ratio of 5:1, presenting as a refined plate-like shape with a certain curvature, as the Fe content increases to 2.0 wt.%. Mn alters the phase reactions and increases the threshold of the Fe content required for β-Al15(FeMn)3Si2, limiting the formation and growth of them simultaneously in time and space. The enrichment of Mn atoms and solute diffusion at the growth front of β-Al15(FeMn)3Si2, as well as the strong atomic-binding ability, can deflect the growth direction of β-Al15(FeMn)3Si2 for it to have a certain curvature. Additionally, the enriched Mn atoms easily form α-Al15(FeMn)3Si2 and cause the long β-Al15(FeMn)3Si2 to be broken and refined to further reduce the damages caused to the alloy’s performance. Ultimately, the maximum length and mean aspect ratio can be effectively reduced to 46.2% and 42.0%, respectively, while the mean curvature can be noticeably increased by 3.27 times with the addition of Mn.