The crack propagation behavior of Al containing Mg–Si clusters is investigated using molecular dynamics (MD) simulations to demonstrate the relationship between the natural aging time in Al–Si–Mg alloys and ductility. Experimental results show that the elongation at failure decreases with natural aging. There are few studies on the relationship between natural aging and ductility because of the difficult observation of Mg–Si clusters. To solve the difficulty, cracked Al containing Mg–Si clusters of varying sizes are assumed for the MD simulations. A larger Mg–Si cluster in Al results in earlier crack opening and dislocation emission. Moreover, as the Mg–Si cluster size increases, the stress near the crack tip becomes more concentrated. This causes rapid crack propagation, a similar effect to that of crack tip sharpening. As a result of long-term natural aging, the cracks expand rapidly. The influence of geometry is also investigated. Crack lengthening and thickness reduction negatively impact the fracture toughness, with the former having a larger impact than the latter. Although there are several discrepancies in the practical deformation conditions, the simulation results can help to more thoroughly understand natural aging in Al–Si–Mg alloys.