Single-molecule electronics offer a unique strategy for the miniaturization of electronic devices. However, the existing experiments are limited to the conventional molecular junctions, where a molecule anchors to the electrode pair with linkers. With such a rod-like configuration, the minimum size of the device is defined by the length of the molecule. Here, by incorporating a single molecule with two single-layer graphene electrodes, we fabricated layer-by-layer single-molecule heterojunctions called single-molecule two-dimensional van der Waals heterojunctions (M-2D-vdWHs), of which the sizes are defined by the thickness of the molecule. We controlled the conformation of the M-2D-vdWHs and the cross-plane charge transport through them with the applied electric field and established that they can serve as reversible switches. Our results demonstrate that the M-2D-vdWHs, as stacked from single-layer 2D materials and a single molecule, can respond to electric field stimulus, which promises a diverse class of single-molecule devices with unprecedented size.