Single-molecule conductance of a B-N substituted phenanthrene derivative and its isoelectronic C=C counterpart was investigated by the scanning tunneling microscopy break junction (STM-BJ) technique. The incorporation of the B-N motif results in a better single-molecule conductivity than the C=C analogue. Furthermore, the Lewis acid-base reaction between F- and the B atom of the B-N motif leads to a decrease of the conductance of the BN derivative, which can be understood due to the shifting of the energy positions of the LUMO, as revealed by quantum transport calculations, even though the HOMO-LUMO gap decreases in the B-F Lewis acid-base. These findings provide insights for modulating electron transport properties by isoelectronic structure design. The B-N isoelectronic substituted structure could be a feasible way to design single-molecule devices such as switches and chemical sensors.