Using ab initio calculations, we demonstrate the strong influence of valence electron concentration (VEC) on the local atomic structure and electronic properties of Mo6S9-xIx (x = 0-9) nanowires (NWs). We find new atomic models of the NWs with unique decoration of S/I atoms that are more stable than reported earlier. The electronic and mechanical properties of these NWs are in good agreement with experiments. Further we tuned VEC by either varying the number of I atoms or adding S/Li atoms to obtain semiconducting Mo6S3I6, Mo6S2I8, Li6Mo6S9, and Li3Mo6S6I3 NWs, all of which have VEC of 24 and isolated Mo6 octahedral units, as observed in bulk cluster compounds. These results suggest that VEC is the thumb rule to design and tune the atomic structure and electronic properties of Mo-S-I cluster based nanostructures. © 2015 American Chemical Society.