Chemical oxidation of multilayer graphene grown on silicon carbide yields films exhibiting reproducible characteristics, lateral uniformity, smoothness over large areas, and manageable chemical complexity, thereby opening opportunities to accelerate both fundamental understanding and technological applications of this form of graphene oxide films. Here, we investigate the vertical inter‐layer structure of these ultra‐thin oxide films. X‐ray diffraction, atomic force microscopy, and IR experiments show that the multilayer films exhibit excellent inter‐layer registry, little amount (<10%) of intercalated water, and unexpectedly large interlayer separations of about 9.35 Å. Density functional theory calculations show that the apparent contradiction of “little water but large interlayer spacing in the graphene oxide films” can be explained by considering a multilayer film formed by carbon layers presenting, at the nanoscale, a non‐homogenous oxidation, where non‐oxidized and highly oxidized nano‐domains coexist and where a few water molecules trapped between oxidized regions of the stacked layers are sufficient to account for the observed large inter‐layer separations. This work sheds light on both the vertical and intra‐layer structure of graphene oxide films grown on silicon carbide, and more in general, it provides novel insight on the relationship between inter‐layer spacing, water content, and structure of graphene/graphite oxide materials.