In situ low-temperature scanning tunneling microscopy and near-edge x-ray absorption spectroscopy measurements have been used to investigate the molecular orientation of 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) thin films at the interface of organic heterojunctions of PTCDA on copper(II) phthalocyanine (CuPc). On the CuPc monolayer on highly oriented pyrolitic graphite, PTCDA molecules form a well-ordered in-plane herringbone structure with their molecular plane parallel to the substrate surface. The formation of multiple in-plane hydrogen bonding between neighboring PTCDA molecules is responsible for the flat-lying PTCDA on CuPc monolayer, and gives rise to the lying-down orientation of PTCDA thin films on both standing-up and lying-down CuPc thin films, as well as on Au(111) passivated by a self-assembled monolayer of octane-1-thiol.