Graphene oxide (GO) has attracted intense interest for its use as a precursor material for the mass production of graphene-based materials, which hold great potential in various applications. Insights into the structure of GO and reduced GO (RGO) are of significant interest, as their properties are dependent on the type and distribution of functional groups, defects, and holes from missing carbons in the GO carbon lattice. Modeling the structural motifs of GO can predict the structural evolution in its reduction and presents promising directions to tailor the properties of RGO. Two general reduction approaches, chemical and thermal, are proposed to achieve highly reduced GO materials. This review introduces typical chemical oxidation methods to produce GO from pure graphite, then summarizes the modeling progress on the GO structure and its oxidation and reduction dynamics, and lastly, presents the recent progress of RGO preparation through chemical and thermal reduction approaches. By summarizing recent studies on GO structural modeling and its reduction, this review leads to a deeper understanding of GO morphology and reduction path, and suggests future directions for the scalable production of graphene-based materials through atomic engineering.