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Dispersing graphene nanosheets in polymer-derived ceramics (PDCs) has become a promising route to produce exceptional mechanical and functional properties. To reveal the complex nanodomain structures of graphene–PDC composites, a novel reduced graphene oxide aerogel embedded silicon oxycarbide (RGOA-SiOC) nanocomposite was fabricated bottom-up using a 3D reduced graphene oxide aerogel as a skeleton followed by infiltration of a ceramic precursor and high-temperature pyrolysis. The reduced graphene oxide played a critical role in not only the form of the free carbon phase but also the distribution of SiO_xC_4−x structural units in SiOC. Long-ordered and continuous graphene layers were then embedded into the amorphous SiOC phase. The oxygen-rich SiO_xC_4−x units were more prone to forming than carbon-rich SiO_xC_4−x units in SiOC after the introduction of reduced graphene oxide, which we attributed to the bonding of Si atoms in SiOC with O atoms in reduced graphene oxide during the pyrolysis process.