Intermetallic phases were found to influence the anodic oxidation and corrosion behavior of 5A06 aluminum alloy. Scattered intermetallic particles were examined by scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS) after pretreatment. The anodic film was investigated by transmission electron microscopy (TEM), and its corrosion resistance was analyzed by electrochemical impedance spectroscopy (EIS) and Tafel polarization in NaCl solution. The results show that the size of Al-Fe-Mg-Mn particles gradually decreases with the iron content. During anodizing, these intermetallic particles are gradually dissolved, leading to the complex porosity in the anodic film beneath the particles. After anodizing, the residual particles are mainly silicon-containing phases, which are embedded in the anodic film. Electrochemical measurements indicate that the porous anodic film layer is easily penetrated, and the barrier plays a dominant role in the overall protection. Meanwhile, self-healing behavior is observed during the long immersion time.