Vibrational dynamics governs the fundamental properties of molecular crystals, shaping their thermodynamics, mechanics, spectroscopy, and transport phenomena. However desirable, the accurate first-principles calculation of solid-state vibrations (i.e. phonons) stands as a major computational challenge in molecular crystals characterized by many atoms in the unit cell and by weak intermolecular interactions. Here, we propose a formulation of harmonic lattice dynamics based on a natural basis of molecular coordinates consisting of rigid-body displacements and intramolecular vibrations. This enables a sensible minimal molecular displacement approximation for the calculation of the dynamical matrix, combining isolated molecule calculations with only a small number of expensive crystal supercell calculations, ultimately reducing the computational cost by up to a factor of 10. The comparison with reference calculations demonstrates the quantitative accuracy of our method, especially for the challenging and dispersive low-frequency region for which it is designed. Our method provides an excellent description of the thermodynamic properties and offers a privileged molecular-level insight into the complex phonon band structure of molecular materials.