When two planar atomic membranes are placed within the van der Waals distance, the charge and heat transport across the interface are coupled by the rules of momentum conservation and structural commensurability, leading to outstanding thermoelectric properties. Here we show that an effective ``interlayer phonon drag″ determines the Seebeck coecient (S) across the van der Waals gap formed in twisted bilayer graphene (tBLG). The cross-plane thermovoltage, which is nonmonotonic in both temperature and density, is generated through scattering of electrons by the out-of-plane layer breathing (ZO'/ZA(2)) phonon modes and differs dramatically from the expected Landauer-Buttiker formalism in conventional tunnel junctions. The tunability of the cross-plane Seebeck effect in van der Waals junctions may be valuable in creating a new genre of versatile thermoelectric systems with layered solids.