Molecular alignment control of non-peripherally hexyl-substituted phthalocyanine (C6PcH2) in thin films has been investigated. Planar alignment of C6PcH2 molecules in the thin film was induced by bar-coating, and homeotropic alignment was induced by the thermal annealing of C6PcH2 thin film covered with a poly(vinylphenol) layer. The threedimensional molecular packing structure in the uniaxially planar oriented thin film was clarified by the grazing incidence wide-angle X-ray scattering (GIWAXS) technique with sample rotation. The quality of the molecularly oriented thin film was discussed based on the X-ray rocking curve measurement and simulation utilizing the single-crystal structure of C6PcH2. The molecular alignment in the homeotropically oriented thin film was also clarified by the temperature controlled GIWAXS measurement. The origin of inducing homeotropic alignment in the thin film was discussed based on the molecular alignment in the LC phase.