In recent years, regulating organic functional molecules has gradually achieved much attention in field of materials due to its significant contribution in aspects of improving the charge carrier mobility of nanometer optoelectronic device. Molecular configurations and assembly structures of vanadyl phthalocyanine (VOPc) are systemically investigated on pristine and oxidized Cu(110) surfaces by using low temperature scanning tunneling microscopy. In the initial deposition stage, two molecular adsorption configurations, referring to O-up and O-down, randomly distribute on the pristine Cu(110) surface. By oxidizing Cu(110) at different oxygen ambience and substrate temperatures, two different copper oxide structures were obtained, i.e., CuO-(2×1) and Cu<sub>5</sub>O<sub>6</sub>-c(6×2). VOPc molecules were 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<sup>0</sup>each other. On Cu<sub>5</sub>O<sub>6</sub>-c(6×2), the O-down and O-up molecules isolatedly adsorb at the initial coverage. As the coverage increasing, molecular assembly film gradually forms with a parallelogram-shaped unit cell that involves only the O-up molecules. The molecular film exhibits two distinct molecular orientations that rotate by about 42<sup>0</sup> with each other. The dipole-dipole interaction drives the configuration transition from the O-up to O-down configurations. The O-down VOPc molecules of the second layer tend to be adsorbed on the molecular membrane supported by the Cu<sub>5</sub>O<sub>6</sub>-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 aspects of modifying configurations and orbital distributions of adsorbed molecules that would impact the charge transport in molecular films during fabricating electronic devices.