The nanoscale moirépattern formed at 2D transition-metal dichalcogenide crystal (TMDC) heterostructures provides periodic trapping sites for excitons, which is essential for realizing various exotic phases such as artificial exciton lattices, Bose−Einstein condensates, and exciton insulators. At organic molecule/TMDC heterostructures, similar periodic potentials can be formed via other degrees of freedom. Here, we utilize the structure deformability of a 2D molecular crystal as a degree of freedom to create a periodic nanoscale potential that can trap interlayer excitons (IXs). Specifically, two semiconducting molecules, PTCDI and PTCDA, which possess similar band gaps and ionization potentials but form different lattice structures on MoS 2 , are investigated. The PTCDI lattice on MoS 2 is distorted geometrically, which lifts the degeneracy of the two molecules within the crystal's unit cell. The degeneracy lifting results in a spatial variation of the molecular orbital energy, with an amplitude and periodicity of ∼0.2 eV and ∼2 nm, respectively. On the other hand, no such energy variation is observed in PTCDA/MoS 2 , where the PTCDA lattice is much less distorted. The periodic variation in molecular orbital energies provides effective trapping sites for IXs. For IXs formed at PTCDI/MoS 2 , rapid spatial localization of the electron in the organic layer toward the interface is observed, which demonstrates the effectiveness of these interfacial IX traps.