The realization of molecular devices via metal–molecule–metal junctions necessitates the fabrication of a steady molecular bridging structure, where the number of bridging structures should be fixed. This study investigated a new molecular bridging method using migrations of gold atoms on static nanogap electrodes. First, static nanogap electrodes with a large gap size were fabricated for bridging molecules, and the gap size was controlled through the applied bias voltage after the electrodes were coated with molecules. Similar to a mechanically controlled break junction (MCBJ), nanogap electrodes coated with thiol or dithiol molecules were continuously elongated and contracted under applied bias voltages. As the size of the nanogap varied, the electric properties of a single Au–benzene-dithiol (BDT)–Au junction, which have been previously evaluated using the MCBJ method, were clearly determined. Although MCBJ and scanning tunneling microscopy break junctions have been used to measure the electric properties of single molecules, these techniques are difficult to apply in integrated molecular devices. The proposed method is expected to be applicable to minuscule molecular devices with its ability to control gap sizes in static nanogap structures.