DFT was used to analyze the molecular and electronic structures of the mono, di‐ and tri‐substituted isomers of [Mo(CO)6‐n(SiX)n] (where, X=O, S, Se, Te) and they were compared to the Mo(CO)6 complex. The total energy of all the complexes indicates that the trans isomer is slightly more stable than the cis isomer, but the stability of the fac and mer isomers is comparable. The HOMO‐LUMO energy gap of the complexes was determined and it indicated that the energy gap of the newly designed complexes is smaller than that of the parent complex Mo(CO)6 (1), ranging from 3.45–5.08 eV for the complexes 2–21. The FMO analysis of 2–21 showed that they are more reactive than complex 1. Insights on the bonding nature of these complexes are provided by the NPA, NBO, and EDA studies. The bond contribution from the Si atom in the Mo−Si bond is greater than that from the Mo atom, based on the NBO study. However, the C atom contributes more to the Mo−CO bond as well. Atomic charges on the Mo atom have a higher negative charge and the Si atom shows a positive charge in all the complexes. This study provides valuable information about the isolobal and isoelectronic nature of different substitutions of Si−X bonds at different positions instead of CO molecule in [Mo(CO)6].