Developing effective structural design strategies for regulating charge transport is a central focus in molecular electronics. The interplay between molecular symmetry and orbital distribution, facilitated by heteroatom substitution, presents opportunities for direct modulation in both resonant and off-resonance tunneling processes. In this study, scanning tunneling microscopy-break junction techniques and the first-principles calculations are employed to investigate the electronic properties of boron-embedded acenes. Compared to the parent acene, boron incorporation shifts the transport-dominating molecular orbital from a centrally localized distribution to a delocalized configuration across the orthogonal molecular backbone. This shift results in a 10-fold increase in conductance in the off-resonance region near zero bias and a 50-fold enhancement in conductance through near-resonant tunneling at high bias voltages. Notably, expanding the central acene fragment increases orbital asymmetry within molecular junctions, thereby compromising transport efficiency. However, applying a bias voltage gradually mitigates the symmetry-breaking effect, leading to through-backbone orbital distribution and a recovery in the near-resonant tunneling conductance. This orthogonal control of electronic transport channels provides a distinct strategy for the effective regulation of molecular conductance.