The bending properties of 6000 series Al alloys are affected by the precipitates, shear band generation, preferred orientation, and residual stress distribution. Such alloys are characterized by initial cracks of extruded profiles that initiate at depths of 100–200 μm. Studies have used TEM to investigate the effect of precipitates. However, it is also important to evaluate the energetic stability of the grain boundaries and grain matrix around the crack origin at a micro level. To clarify the crack initiation mechanism, we considered the kernel average misorientation (KAM) and sigma (Σ) value at the crack initiation point. In cross sections from the surface region up to a depth of 400 μm, A6061 showed 15% more low-order Σ values of 3, 5, and 7, indicating that it had an energetically stable and strong interface compared to A6005C. The KAM map and Σ value of the surrounding area were obtained using electron backscatter diffraction measurements. The KAM map indicated that the initial crack occurred at the grain boundary with a high strain concentration and high Σ value. STEM-EDS results revealed precipitates in the grain matrix of AlMgSiCu-based Q or Q’ compounds. Their number density and PFZ width were almost the same, and they had only a small effect on crack initiation. However, the morphology of the precipitates in A6061 was smaller than that in A6005C; this may affect the strain distribution in the grain matrix. Thus, we focused on the energetic stability of the grain boundaries and grain matrix and found that cracks initiated at unstable grain boundaries with a large Σ value where strain was concentrated when a tensile force was applied.