Nonequilibrium structures in nanocomposites provide possibilities to modulate the organization of nanofillers beyond the phase diagram and to fabricate functional materials with targeted properties. However, multicomponent systems, such as nanocomposites, have complex phase diagrams and kinetic pathways. Here, effects of two critical parameters, nanoparticle (NP) size and supramolecular morphology, were systematically evaluated in NP/supramolecule blends. NPs in the size range of 5-25 nm were assembled in cylindrical or lamellar supramolecular nanocomposite thin films with periodicities of 20-30 nm under solvent vapor annealing and rapid solvent removal conditions. The ratio of particle size to supramolecular periodicity was tuned between 0.17 and 1.25. The results showed that the vertical diffusion of NPs toward the film surface depends on the matrix morphology. NP surface migration is more prominent in cylindrical thin films than in lamellar thin films. This is mainly attributed to the higher energetic barriers for interdomain diffusion in lamellar morphology. Supramolecular nancomposite thin films with ordered structures can be obtained by balancing the size-dependent NP diffusivity and energetic factors affecting NP diffusion during the annealing process for a range of NP sizes. Present studies give insight into how to manipulate the assembly kinetics to access targeted morphologies in nanocomposite thin films.