Although the effect of Sc addition on the nano-phase transformation of precipitates in Al-Mg-Si alloys has been evaluated in the literature, the properties and related explanation based on the multi-scale microstructures are less available yet. In this paper, the hierarchical microstructures and properties of peak-aging Al–0.5 Mg–0.4Si (wt.%) alloy (AlMgSi) and AlMgSi alloy microalloying with 0.4 wt% Sc (AlMgSiSc) were investigated by atomically-resolved transmission electron microscopy and atom probe tomography. The results show that a certain number of Sc solutes exist in the Al matrix, forming a solid solution strengthening matrix with reduced corrosion susceptibility. In addition, the strengthening and toughening of AlMgSiSc are associated with the formation of primary Al3Sc dispersoids, which cause dispersion strengthening and fine-grain strengthening. Moreover, the precipitate free zones (PFZs) containing Sc solutes were observed in the AlMgSiSc, leading to the excellent resistance to intergranular corrosion and elongation due to the smaller width and higher corrosion potentials of PFZ compared with AlMgSi. The Sc solutes can significantly promote the precipitation of GP zones and solute clusters. Further study reveals that smaller-scale precipitates, GP zones, and solute clusters have enrichment of Sc as well, thereby bringing out remarkable precipitation hardening to AlMgSiSc.