Establishing homojunctions at the molecular level between different but physicochemically similar phases belonging to the same family of materials is an effective approach to promoting the photocatalytic activity of polymeric carbon nitride (CN) materials. Here, we prepared a CN material with a uniform distribution of homojunctions by combining two synthetic strategies: supramolecular assemblies as the precursor and molten salt as the medium. We designed porous CN rods with triazine-heptazine homojunctions (THCNs) using a melem supramolecular aggregate (Me) and melamine as the precursors and a KCl/LiBr salt mixture as the liquid reaction medium. The triazine/heptazine ratio is controlled by varying the relative amounts of the chosen precursors, and the molten salt treatment enhances the structural order of the interplanar packing units for the THCN skeleton, leading to rapid charge migration. The resulting built-in electric field induced by the triazine-heptazine homojunction enhances photogenerated charge separation; the optimal THCN catalyst exhibits an excellent H2 evolution rate via photocatalytic water splitting, which is ∼24 times as high as that of reference bulk CN, with long-term stability.