Metal‐free boron‐based catalysts such as boron oxide (B2O3) and boron nitride (h‐BN) are promising catalysts for the methane oxidation to HCHO and CO. The B2O3 catalyst contains various probable boron sites (B1 to B6), which may be responsible for methane oxidation. In this work, we utilized density functional theory to compare two relevant geometrically identical boron sites (B2 and B4) for their reactivities. The two sites are explored in‐detail for the conversion of methane to formaldehyde (M2F), carbon monoxide and carbon dioxide. The B4 site activates the methane C−H bond easily as compared to the B2 site. In M2F conversion, the rate‐determining step for the B2 site is the co‐activation of dioxygen and methane, whereas over the B4 site, formaldehyde formation is the rate‐determining step. The computationally‐determined RDS for the B4 site coincides well with the reported experiments. It is further revealed that this site also prefers the formation of CO over CO2, which is in‐line with the experiments in literature. It is also shown through orbital analysis that methanol formation does not occur during methane oxidation. We employed descriptors such as condensed Fukui functions and global electrophilicity index to chemically distinct these twin sites.