Density functional theory approaches are employed to elucidate the structural features and electronic properties of cisdioxidomolybdenum(VI) complexes with water, 8-hydroxyquinoline and 4-benzoyl-3-methyl-1-phenyl-2-pyrazolin-5-one. Geometrical parameters are optimized using B3PW91, B3LYP functionals in conjunction with def2-TZVP, LanL2DZ and 6-311+G basis sets. Computed results show that the complex energetically prefers a pseudo-pentagonal bipyramidal shape in the ground state. The nature of intramolecular interactions between Mo(VI) and ligands is evaluated by analyzing the natural bond orbital and quantum theory of atoms in molecules. The Mo–OH2 interaction is rather weak with an average distance of 2.445 Å and a very low Mayer bond order of 0.235. The vibrational signatures and vertical electronic transitions of some excitations are examined and compared to available experimental data. The most favorable sites for electrophilic, nucleophilic attack or protonation were also identifed using the noncovalent interaction method.