The creation of novel surface morphologies through thin-film patterning is important from a scientific and technological viewpoint in order to control specific surface properties. The pulsed-plasma polymerization of thin nanocomposite films, including maleic anhydride (MA) and cellulose nanocrystals (CNC), may result in different metastable film morphologies that are difficult to control. Alternatively, the transformation of deposited plasma films into crystalline structures introduces unique and more stable morphologies. In this study, the structural rearrangements of plasma-polymerized (MA+CNC) nanocomposite films after controlled hydrolysis in a humid atmosphere were studied, including effects of plasma conditions (low duty cycle, variable power) and monomer composition (ratio MA/CNC) on hydrolysis stability. The progressive growth of crystalline structures with fractal dendrites was observed in confined thin films of 30 to 50 nm. The structures particularly formed on hydrophilic substrates and were not observed before on the more hydrophobic substrates, as they exist as a result of water penetration and interactions at the film/substrate interface. Furthermore, the nucleating effect and local pinning of the crystallites to the substrate near CNC positions enhanced the film stability. The chemical structures after hydrolysis were further examined through XPS, indicating esterification between the MA carboxylic acid groups and CNC surface. The hydrolysis kinetics were quantified from the conversion of anhydride groups into carboxylic moieties by FTIR analysis, indicating enhanced hydrolytic stability of p(MA+CNC) nanocomposite films relative to the pure p(MA) films.