On the basis of computational and experimental approaches, we provide molecular-level insights into melamine cyanurate (M-CA) self-assembly in aqueous solution and identify corresponding mechanisms of aggregation. Our analysis implies that small M-CA molecular complexes are stabilized predominantly via aromatic π−π-stacking rather than by formation of hydrogen bonds. We demonstrate that variation of the [M]/[CA] component concentration ratio results in a smooth change in the structure of the critical nuclei from more disordered in the excess of M to more crystal-like in the excess of CA. This behavior can indicate that the process of M-CA nucleation in aqueous solutions could be altered between classical and nonclassical mechanisms depending on the local [M]/[CA] concentration ratio, which could be prospective for the programmable design of functional supramolecular materials.