Obstructed thermal transport across interfaces is the main cause of serious heat dissipation issues in electronics. Analogous to heterointerface in heterostructure, homointerface is another widely existing interface, such as grain boundary (GB) in polycrystal. Through nonequilibrium molecular dynamics simulations, we investigated the thermal transport across armchair–zigzag graphene GB homointerfaces and reported the ultrahigh interfacial thermal conductance (ITC) in the order of 10 GW/m2K induced by well-matched phonons, much larger than those of heterointerfaces with mismatched phonons. By comparing four homointerfaces with different interfacial atomic structures, we pointed out a significant underestimation of ITC in previous works commonly using the “fly-head” structure. At 300 K, the ITC of the homointerface with the most energetically favorable structure is 30% higher than that of the “fly-head” homointerface. Spectral decomposition of ITC demonstrated suppressed phonon transmission in the full frequency range in the “fly-head” homointerface. Atom-resolved analysis unraveled that the “fly-head” homointerface shows aggregated stress distribution and thus significant modification in atomic vibrations near the interface, leading to a poorer match of phonon density of states. Furthermore, we found that the inelastic phonon transport is overwhelmed by elastic processes at the homointerface, as evidenced by the temperature independence of ITC at elevated temperatures and the consistent spectral heat flux of the interface and bilateral regions. This work provides insight into the microscopic thermal transport mechanism of homointerfaces.