The structural, electronic, and magnetic properties of molybdenum-based nanowires have been actively investigated for their potential applications in nanodevices; however, further advancement is hindered by incomplete knowledge of the electronic and atomic structures of Mo6S3I6. To facilitate further development of Mo6S3I6 nanowire devices, we propose possible atomic structures and corresponding electronic properties of Mo6S3I6 nanowires based on density functional theory. We explored various combinations of atomic structures by changing the positions of sulfur and iodine atoms linked to the two Mo6 octahedra in the Mo6S3I6 unit cell. We found two stable local energy minima structures characterized by elongation of the wire length, and therefore propose 28 possible atomic configurations. We calculated band structures of the newly proposed atomic models and found three structures that behaved as conductors. According to our compositional ordering structural analysis, we concluded that (i) periodic distortion of the bond lengths influences the behavior of the electrons in the system, (ii) the role of sulfur atoms in the bridging plane is important for intramolecular charge transport due to delocalized charge differences, and (iii) the electronic band gap energy is proportional to the integrated Mo-S bonding orbital energy.