Molecular self-assembly can be a powerful strategy for fabricating dynamic two-dimensional (2D) nanomaterials. However, formulating a rational design principle that meets the stringent thermodynamic and kinetic requirements for uniform in-plane growth, while also allowing dynamic structural rearrangement, presents a considerable challenge. We report a hydrophobic core-substituted naphthalenediimide that self-assembles in water−dioxane mixtures to form a pair of 2D polymorphs, with distinct morphological, optical, and surface characteristics. Changing the solvent composition or temperature prompts an in situ transformation between the two polymorphs in solution. A comprehensive structural investigation using solid-state NMR spectroscopy, X-ray, and electron diffraction analyses reveals not only the nature of molecular packing and noncovalent (n → π* and π-stacking) interactions stabilizing each 2D polymorph but also the role of weak solvent−solute interactions in driving polymorphic interconversion. Variations in the perfluoroalkyl side chains arrangements on the exposed 2D surface of the two polymorphs lead to distinct solvent−solute interactions at the solid−liquid interface, which affects the surface free-energy and relative stability in different solvent compositions. Further, the entropy change associated with surface ordering of perfluoroalkyl side chains and desolvation dictates thermal reorganization between the polymorphs. How changes in dioxane−water microheterogeneity with solution composition and temperature may affect these weak solvent−solute interactions and the phase equilibrium is also discussed.