Molecule-electrode interfaces play a pivotal role in defining the electron transport properties of molecular electronic devices. While extensive research has concentrated on optimizing molecule-electrode coupling (MEC) involving electrode materials and molecular anchoring groups, the role of the molecular backbone structure in modulating MEC is equally vital. Additionally, it is known that the incorporation of heteroatoms into the molecular backbone notably influences factors such as energy levels and conductive characteristics. In this work, we report a series of molecular wires that are organized in donor-acceptor-donor configurations, with distinct chalcogen substitutions, including oxygen (BOD), sulfur (BTD), and selenium (BSD). We investigated the electron transport properties using the scanning tunneling microscope break junction (STM-BJ) technique. Our results revealed that both the single-molecule conductance and the junction evolution feature are impacted by the heteroatoms in the benzo(chalcogen)diazole cores. Furthermore, current-voltage (I-V) experiments, combined with theoretical analyses, suggest that MEC plays a dominant role in modulating electron transport behaviors. Overall, our findings provide important insights into the interface-mediated charge transport exerted by chalcogen atoms within molecular devices, thereby enhancing the fundamental comprehension of these critical interactions.