Controlling polymorphism, namely, the occurrence of multiple crystal forms for a given compound, is still an open technological challenge that needs to be addressed for the reliable manufacturing of crystalline functional materials. Here, we devised a series of 13 organic crystals engineered to embody molecular fragments undergoing specific nanoscale motion anticipated to drive cooperative order–disorder phase transitions. By combining polarized optical microscopy coupled with a heating/cooling stage, differential scanning calorimetry, X-ray diffraction, low-frequency Raman spectroscopy, and calculations (density functional theory and molecular dynamics), we proved the occurrence of cooperative transitions in all the crystalline systems, and we demonstrated how both the molecular structure and lattice dynamics play crucial roles in these peculiar solid-to-solid transformations. These results introduce an efficient strategy to design polymorphic molecular crystalline materials endowed with specific molecular-scale lattice and macroscopic dynamics.