There is growing interest in creating solids that are responsive to various stimuli. Herein we report the first molecular-level mechanistic picture of the thermochromic polymorphic transition in a series of MAN-NI dyad crystals that turn from orange to yellow upon heating with minimal changes to the microscopic morphology following the transition. Detailed structural analyses revealed that the dyads assemble to create an alternating bilayer type structure, with horizontal alternating alkyl and stacked aromatic layers in both the orange and yellow forms. The observed dynamic behavior in the solid state moves as a yellow wavefront through the orange crystal. The overall process is critically dependent on a complex interplay between the layered structure of the starting crystal, the thermodynamics of the two differently colored forms, and similar densities of the two polymorphs. Upon heating, the orange form alkyl chain layers become disordered, allowing for some lateral diffusion of dyads within their own layer. Moving to either adjacent stack in the same layer allows a dyad to exchange a head-to-head stacking geometry (orange) for a head-to-tail stacking geometry (yellow). This transition is unique in that it involves a nucleation and growth mechanism that converts to a faster cooperative wavefront mechanism during the transition. The fastest moving of the wavefronts have an approximately 38° angle with respect to the long axis of the crystal, corresponding to a nonconventional C-H···O hydrogen bond network of dyad molecules in adjacent stacks that enables a transition with cooperative character to proceed within layers of orange crystals. The orange-to-yellow transition is triggered at a temperature that is very close to the temperature at which the orange and yellow forms exchange as the more stable, while being lower than the melting temperature of the original orange, or final yellow, solids.