Bipolar molecules incorporating donor and acceptor components within a single molecule create exciting device opportunities due to their possible use as nanoscale p-n heterojunctions. Here we report a direct characterization of the internal electronic structure of a single bipolar molecular heterojunction, including subnanometer features of the intramolecular donor-acceptor interface. Angstrom-resolved scanning tunneling spectroscopy was used to map the energy levels and spatial extent of molecular orbitals across the surface of an individual bipolar molecule, bithiophene naphthalene diimide (BND). We find that individual BND molecules exhibit type II heterojunction behavior with orbital energy shifts occurring over subnanometer intramolecular interface distances. Comparison of this behavior with first-principles theoretical modeling provides new insights into the optimization of these molecular systems.