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Interaction of energetic ion beam with matter results in atomic excitation and ionization of matter which consequently leads to occurance of the characteristic X-rays fluorescence. In the interaction of energetic molecular beam with matter, the unique phenomena of “Vicinage effect” and “Coulomb explosion” have already been observed and reported. In this research work, the interaction of molecular ion beam with targets of different atomic numbers was investigated. For this purpose, the yields of characteristic X-rays due to interaction of H2+ molecular ion beam with the selected targets were compared with those due to interaction of H+ atomic beam with the same targets. To accomplish this, atomic and molecular beams in the energy range of 1 to 1.4 MeV/u were used to irradiate targets of different atomic numbers, including Cu, Mn and Al. For Mn and Cu. The measured yields of the characteristic X-rays due to the irradiation by the atomic and molecular beams were found to be approximately the same. However, for the Al target, a significant difference was observed for the X-ray characteristic yields due to the irradiation by the atomic and molecular beams.