The purpose of this work is the structural analysis of graphene oxide (GO) and by means of a new structural model to answer the questions arising from the Lerf–Klinowski and the Lee structural models. Surface functional groups of GO layers and the oxidative debris (OD) stacked on them were investigated after OD was extracted. Analysis was performed successfully using Fourier transform infrared spectroscopy (FTIR), ultraviolet-visible spectroscopy (UV-Vis), X-ray photoemission spectroscopy (XPS), energy-dispersive X-ray spectroscopy (EDX), Raman spectroscopy, solid-state nuclear magnetic resonance spectroscopy (SSNMR), standardized Boehm potentiometric titration analysis, elemental analysis, X-ray diffraction (XRD), thermogravimetric analysis (TGA), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). The analysis showed that graphene oxide layers, as well as oxidative debris contain different functional groups such as phenolic –OH, ketone, lactone, carboxyl, quinone and epoxy. Based on these results, a new structural model for GO layers is proposed, which covers all spectroscopic data and explains the presence of the other oxygen functionalities besides carboxyl, phenolic –OH and epoxy groups.