The significance of protein aggregation has been extensively studied in biomedical and food research. While biomaterials, such as soy protein, as green material alternatives, have gained enormous attentions in various industrial and engineering fields, the roles of protein aggregation in material properties and functionalities are still insufficiently understood, which will be the main focus of this study. In this study, soy protein isolate (SPI) with different aggregated structures, was investigated as a functional modifier to tune the microstructures, and ferroelectric properties of poly(vinylidene fluoride) (PVDF). The aggregated structures of SPIs were obtained via various controlled denaturation processes, including heat treatment, high-energy sonication, and usage of denaturation agents. Denatured SPIs were then applied to polymer matrices. It was found that SPI aggregation and SPI-PVDF interactions were strongly subjected to the denaturation conditions, as well as properties of polymer matrix, which led to distinctive morphologies and structures of the resulting PVDF/SPI films. The changes in microstructures consequently caused the variation of ferroelectric properties of the films, leading to different dielectric energy storage performances.