The gluten-free food market is growing worldwide. Zein is a promising gluten substitute in the gluten-free system due to its similar viscoelastic properties to gluten. However, a few existing reviews are limited to the zein characteristics and the application of zein in gluten-free bread and noodles while lacking a comparison of basis information between zein and gluten and the application in other foods, like meat analogue. We compared the structure of zein and gluten at the molecular level to employ zein better in gluten-free food production. The application status of zein in gluten-free systems, the influencing factors of zein functionality, and the potential of zein in meat analogues were summarized comprehensively. The weak elasticity and insufficient gas retention ability are significant challenges for zein dough to produce desired bread. Additives and modifications, such as organic acids and thermal treatment, improve zein functionality by increasing the molecular flexibility or elasticity of the zein network. Future research still needs to focus on increasing zein-starch dough's elasticity and gas retention ability and decreasing zein's high glass transition temperature. Applying zein in meat analogues also requires more attention due to its ability to form fibrous texture.