With the increasing interest in value-added maize products, the interaction of zein with bioactive molecules to become more nutritional and beneficial to human health has gained a lot of attention. To broaden the application of ellagic acid (EA) in maize flour products, we investigated the interaction between zein and EA. The fluorescence quenching type of zein interacting with EA was mainly static quenching through hydrophobic interaction, as demonstrated by quenching behavior modeling, and ultraviolet-visible spectroscopy confirmed the formation of zein–EA complexes. Synchronous fluorescence spectroscopy showed that EA reduced the polarity of zein around tyrosine residues, which were exposed to a more hydrophobic microenvironment. Meanwhile, circular dichroism suggested that EA noticeably changed the secondary structure of zein, which was mainly reflected in the increase of α-helix and β-sheet content and the decrease of random coil content. Finally, the molecular docking simulation found that zein could have five active sites binding to EA and there was hydrogen bond interaction besides hydrophobic interaction. The findings of this study provided a basis for a theory for the interaction mechanism between zein and EA, which could be essential for developing value-added plant-derived protein products using EA as a functional component.