Molybdenum (Mo) is commonly used as the back contact material complying well with the formation of an ohmic contact for chalcogenide thin film solar cells. However, the easy formation of an over-thick MoSe₂ layer between the Cu₂ZnSn(S,Se)₄ absorber and Mo back contact significantly deteriorates the device performance. To overcome the degradation, the effects of thermal treatment on Mo layers have been investigated in this paper. It was found that pre-annealing Mo back contacts is effective to control the growth of interfacial MoSe₂ layer during selenization. Moreover, the thickness of MoSe₂ layer could be conveniently tailored by simply varying the pre-annealing temperature. The work provides direct proof that the appearance of a thin MoO₂ layer on the top of annealed Mo film indeed acts as a temporary barrier to block the over-selenization of Mo back contact.