Abstract: Al–Mg–Si alloys are widely employed in automotive vehicles; however, challenges such as cracking often arise during the hemming process (180° bending). Based on the molecular dynamics simulations and experiments, this study investigated the effects of the size and number of MgSi(Fe) clusters on the mechanical properties of 6xxx Al alloys. The results showed that medium-sized MgSi clusters (containing 10–19 atoms) at the grain boundaries (GBs) enhanced the strength of the GBs, effectively inhibiting crack initiation and significantly suppressing intergranular cracking. In addition, the ductility and brittleness of the model with the Fe-containing phase were significantly affected by the Si/Fe atomic ratio (~0.71). Tensile experiments confirmed that the failure morphology exhibited a distinct brittle fracture when the Si/Fe atomic ratio of the phase was 0.90. The pre-aging treatment promoted the dispersion of solute atoms, thereby reducing the yield strength of the AA6016 Al alloy to ~120 MPa, which improved its hemming performance. Furthermore, preaging facilitated the generation of finer Mg–Si phases at the GBs during bake hardening.