Chalcogenborines (or BX‐doped benzenes, where X=O/S) are interesting for intriguing photophysical and electronic properties. In spite of several advances, origin of their relative thermodynamic stability remains elusive. Now, based on density functional theory (DFT) calculations, we reveal that the relative stability of their mono BX‐doped isomers (here called BX isomers) is in a good relation with the geometry, natural bond orbital partial atomic charges (qs) and bonding energy. Substitution by an electronegative F group in a BX stabilizes boron position significantly than the carbon. On the other hand, substitution by an electropositive SiH3 group imparts small stability to carbon position than the boron. The qs in the parent BX can predict relative stability of the F‐substituted isomers excellently. However, such speculation fails for the SiH3‐substituted isomers due to the close electronegativity of SiH3, C and B. These findings could be helpful for the synthesis of BX derivatives.