A better understanding of the aggregation states of polymer chains in thin films is of pivotal importance for developing thin film polymer devices in addition to its inherent scientific interest. Here we report the preferential orientation of the crystalline lamellae for isotactic polypropylene (iPP) in spin-coated films by grazing incidence of wide-angle X-ray diffraction in conjunction with sum frequency generation vibrational spectroscopy, which provides information on the local conformation of chains at crystal/amorphous interfaces buried in a thin film. The crystalline orientation of iPP, which formed cross-hatched lamellae induced by lamellar branching, altered from a mixture of edge-on and face-on mother lamellae to preferential face-on mother lamellae with decreasing thickness. The orientation of methyl groups at the crystal/amorphous interfaces in the interior region of the iPP films changed, accompanied by a change in the lamellar orientation.