The physical properties of van der Waals materials are highly dependent on their stacking sequences. However, constructing layered materials with specific compositions and desired stackings is challenging. Here we show that a solvent-directed strategy enables targeted stacking in van der Waals metal–organic frameworks, an emerging class of van der Waals materials. By leveraging the tunable metastable states of conjugated ligands through various solvents, and stabilizing these states via metal–ligand coordination, we enable the inheritance of stacking patterns from ligands to van der Waals metal–organic frameworks. Notably, this strategy enables the controlled manipulation of stacking sequences and divergent charge transport regimes in two-dimensional and three-dimensional van der Waals metal–organic framework single crystals, yielding an electrical conductivity of 1,792 S cm−1. These results provide a versatile approach for designing layered materials with programmable stackings and tailored electronic properties.