Starch-based films have been widely researched because of its degradability and low cost. The aim of this work was to evaluate the effect of the addition of protein fibrils, especially the content and the morphology of fibrils, on the properties of starch-based films. Corn starch/whey protein isolate fibrils (CS/WPIF) films were prepared using CS added with different WPIF contents (0.2%, 0.4% and 0.6%) at pH 2.0 or 7.0. The morphology of WPIF was adjusted via changing pH at 2.0 or 7.0, in which WPIF at pH 2.0 was longer than that at pH 7.0 as shown in transmission electron microscopy. The addition of WPIF at pH 2.0 or 7.0 increased the tensile strength, relative crystallinity, and storage modulus of CS films, and reduced the water content, total soluble matter content and water vapor permeability of the films. Compared with the short fibrils at pH 7.0, the long fibrils at pH 2.0 better improved the functional properties of CS films due to a strong network structure of long fibrils. CS/WPIF films with 0.4% WPIF exhibited the best properties, and WPIF at 0.6% reduced the film performance, which might be due to the aggregation of excessive WPIF. Also, CS/WPIF films showed superior antioxidant properties and inhibited the browning of fresh-cut apples during storage.