The thermoelectric properties of polycrystalline copper (Cu) surfaces partially covered with graphene grown by Joule‐heating chemical vapor deposition using scanning thermoelectric microscopy are investigated. Atomic‐resolution atomic force microscopy topographic images of graphene grown on Cu(100) surfaces showed a 1D stripe pattern of Moiré superlattices, while thermoelectric voltage images clearly distinguish wrinkle defects caused by thermal mismatch between graphene and Cu substrate. Regions of different signs were found in the thermoelectric voltage image of the graphene island, which are attributed to the faceted surface of the Cu substrate. In addition, faceted surfaces consisting of low‐ and high‐index Cu surfaces are formed on the Cu grain to minimize the surface energy. Due to these structural changes, charge transfer and chemical interactions at the interface between the graphene and Cu facets affect the electronic structure of the graphene, which is understood as the observed Seebeck coefficients with different signs in the thermoelectric microscopy measurements, which are sensitive to the local density of states.