The electronic structure of bilayer graphene can be altered by creating defects in its carbon skeleton. However, the natural defects are generally heterogeneous. On the other hand, rational bottom-up synthesis offers the possibility of building well-defined molecular cutout of defect-containing bilayer graphene, which allows defect-induced modulation with atomic precision. Here, we report the construction of a molecular defect-containing bilayer graphene (MDBG) with an inner cavity by organic synthesis. Single-crystal x-ray diffraction, mass spectrometry, and nuclear magnetic resonance spectroscopy unambiguously characterize the structure of MDBG. Compared with its same-sized, defect-free counterpart, the MDBG exhibits a notable blue shift of optical absorption and emission, as well as a 9.6-fold brightening of its photoluminescence, which demonstrates that a single defect can markedly alter the optical properties of bilayer graphene.