A deeper understanding of plasma electrolytic oxidation (PEO) can in turn shed light on the evolution of coating structures during such oxidation processes. Here, a three-dimensional (3D) structure of PEO coating was investigated based on the morphologies at different locations in a PEO coating and on the elemental distribution along certain sections. The coating surface was dominated by a crater- or pancake-like structure of alumina surrounded by Si-rich nodules. A barrier layer with a thickness of ~1 μm consisting of clustered cells was present at the aluminum/coating interface. As the coating thickened, the PEO coating gradually evolved into a distinct three-layer structure, which included a barrier layer, an internal structure with numerous closed holes, and an outer layer with a rough surface. During the PEO process, molten zones formed along with the plasma discharges. The volume and lifetime of the molten zones changed with oxidation time. The diversities of cooling rates around the molten zones resulted in structural differences along a certain section of the coating. A growth and discharge model of PEO coatings was established based on the 3D structure of the particular coating studied herein.