Recent progress in organic electronics has attracted interest due to their excellent characteristics that include photovoltaic, light emission, and semiconducting behaviours. Spin-induced properties play important roles in organic electronics, while introducing spin into an organic layer in which spin responses, such as a weak spin-orbital coupling and long spin-relaxation time, allows a variety of spintronic applications to be achieved. However, such spin responses are rapidly attenuated by misalignment in the electronic structure of hybrid structures. We report herein on the energy level diagrams of Ni/rubrene bilayers that can be tuned by an alternating stacking. The band edges of the highest occupied molecular orbital (HOMO) levels were determined to be 1.24 and 0.48 eV relative to the Fermi level for Ni/rubrene/Si and rubrene/Ni/Si bilayers, respectively. This raises a possibility of accumulating electric dipoles at the ferromagnetic/organic semiconductor (FM/OSC) interface, which would inhibit the transfer of spin in the OSC layer. This phenomenon is caused by the formation of a Schottky-like barrier in the rubrene/Ni heterostructures. According to the information about the band edges of the HOMO levels, schematic plots of the HOMO shift in the electronic structure of the bilayers are presented. Based on the lower value of the effective uniaxial anisotropy for Ni/rubrene/Si, the uniaxial anisotropy was suppressed compared to that of rubrene/Ni/Si. The characteristics of the formation of Schottky barriers at the FM/OSC interface have an impact on the temperature-dependent spin states in the bilayers.