This study investigates the interplay between film thickness and the surface and internal morphologies in polymer nanocomposite (PNC) films. The PNC is 25 wt % poly(methyl methacrylate)-grafted silica nanoparticles (NPs) in poly(styrene-ran-acrylonitrile) annealed in the twophase region. At greatest confinement (120 nm), NP surface density remains constant, and lateral phase separation is inhibited upon annealing. For thicker films (240−1400 nm), surface density increases with time before approaching ca. 740 NP/μm 2 , consistent with 2D random close packing. Moreover, lateral domain growth exhibits a dimensional crossover as thickness increases from t 1/2 to t 1/3 , consistent with domain coalescence. Water contact angles decrease upon annealing in agreement with the lateral domain composition. For thickest films (1400−4000 nm), a morphology map summarizes the distinct internal arrangements of NPs: disordered aggregates, continuous vertical pillars, discrete vertical pillars, isolated domains, and random networks. This study of PNC films provides guidance for controlling surface and bulk structure which can lead to improved barrier, mechanical, and transport properties.