Long-range magnetic ordering of two-dimensional crystals can be sensitive to interlayer coupling, enabling the effective control of interlayer magnetism towards voltage switching, spin filtering and transistor applications. With the discovery of two-dimensional atomically thin magnets, a good platform provides us to manipulate interlayer magnetism for the control of magnetic orders. However, a less-known family of two-dimensional magnets possesses a bottom-up assembled molecular lattice and metal-to-ligand intermolecular contacts, which lead to a combination of large magnetic anisotropy and spin-delocalization. Here, we report the pressure-controlled interlayer magnetic coupling of molecular layered compounds via chromium-pyrazine coordination. Room-temperature long-range magnetic ordering exhibits pressure tuning with a coercivity coefficient up to 4 kOe/GPa, while pressure-controlled interlayer magnetism also presents a strong dependence on alkali metal stoichiometry and composition. Two-dimensional molecular interlayers provide a pathway towards pressure-controlled peculiar magnetism through charge redistribution and structural transformation.