Ambipolar organic semiconductors are considered promising for organic electronics because of their interesting electric properties. Many hurdles remain yet to be overcome before they can be used for practical applications, especially because their orientation is hard to control. We demonstrate a method to control the orientation of columnar structures based on a hydrogen (H)-bonded donor-acceptor complex between a star-shaped tris(triazolyl)triazine and triphenylene-containing benzoic acid, using physicochemical nanoconfinement. The molecular configuration and supramolecular columnar assemblies in a one-dimensional porous anodic aluminium oxide (AAO) film were dramatically modulated by controlling the pore-size and by chemical modification of the inner surface of the porous AAO film. In situ experiments using grazing-incidence X-ray diffraction (GIXRD) were carried out to investigate the structural evolution produced at the nanometer scale by varying physicochemical conditions. The resulting highly ordered nanostructures may open a new pathway to effectively control the alignment of liquid crystal ambipolar semiconductors.