In recent years, regulating organic functional molecule has gradually received much attention in the field of materials due to its significant contribution in improving the charge carrier mobility of nanometer optoelectronic device. Molecular configuration and assembly structure of vanadyl phthalocyanine (VOPc) are systemically investigated on pristine and oxidized Cu(110) surface by using low temperature scanning tunneling microscopy. In the initial deposition stage, two molecular adsorption configurations, referring to O-up and O-down, are randomly distributed on the pristine Cu(110) surface. By oxidizing Cu(110) at different oxygen atmospheres and substrate temperatures, two different copper oxide structures are obtained, i.e. CuO-(2×1) and Cu₅O₆-c(6×2). The VOPc molecules are then deposited on both surfaces via thermal evaporation. For the CuO-(2×1) surface, contrastly, extended molecular chains form in the initial adsorption and subsequently the VOPc molecules assemble into an ordered molecular film involving both configurations. The VOPc molecules shows two packing orientations with a rotation angle of about 36° relative to each other. On Cu₅O₆-c(6×2), the O-down and O-up molecules are isolatedly adsorbed at the initial coverage. As the coverage increases, molecular assembly film gradually forms a parallelogram-shaped unit cell that involves only the O-up molecules. The molecular film exhibits two distinct molecular orientations with a rotation angle of about 42° relative to each other. The dipole-dipole interaction drives the configuration transition from the O-up configuration to O-down configuration. The O-down VOPc molecules of the second layer tend to be adsorbed on the molecular membrane supported by the Cu₅O₆-c(6×2) surface. The dipole-dipole interaction between neighboring molecular layers may be responsible for the preferable adsorption of the second-layered molecules. This study suggests the importance of surface oxidization in modifying configurations and orbital distributions of adsorbed molecules that can affect the charge transport in molecular films during fabricating electronic devices.