Silicon oxycarbide (SiOC) is a unique system that can generate various compositions and microstructures via different polymeric precursors and pyrolysis conditions. However, understanding of the atomic structure evolution, such as cluster formation, phase evolution, and atomic coordination, is lacking. In this study, cluster evolution and atomic coordination for different SiOC ceramics pyrolyzed at 1200 °C and 1500 °C were investigated by high energy X-ray diffraction (HE-XRD) and radial distribution function (RDF) analysis. A new Reactive Force Field (ReaxFF) molecular dynamics modeling approach was developed to understand nanocluster separation and early-stage atomic radial coordination. For the first time, we demonstrate that orthorhombic SiO2 forms and converts to growth resistant amorphous SiO2. Cubic β-SiC also forms at lower temperatures than reported, along with a minor amount of hexagonal SiC that has never been reported. The RDF data support such phase evolution understanding. ReaxFF simulation provides direct data on atomic mixing, elemental separation, and effects of precursor molecular structures and compositions, especially in the early stage of the pyrolysis. The simulated RDF data complement the experimental data, revealing the significant presence of C–H bonds along with Si–O and C–C bonds.