A theoretical investigation of molecular, electronic structures and vibrational spectrum for vanadium naphthalocyanine (VONc) was performed based on the optimized geometry at UB3LYP/6–31G(d) level. Unlike the symmetry (D4h) of NiNc, CuNc and ZnNc, the point group of VONc is C4v. By comparing with metallonaphthalocyanines, the order of the bond lengths of the M–N bonds is computed to be NiNc < CuNc < ZnNc < VONc. The Mulliken atomic charges of the central M vary in the same order as the bond lengths. Of the four molecules, VONc has the smallest HOMO–LUMO gap (1.80 eV). Furthermore, accurate and detailed assignment of the vibrational modes were obtained with both calculated potential energy distribution (PED) and assistance of animated pictures produced based on the normal coordinates. In order to make the assignment of the vibrational spectrum more concise and clear, a brand new symbol system was adopted. Experimental incorrect or missed assignments of vibrational modes were corrected or supplemented by comparison of the experimental and computed results of VONc.