Summary Generally, gelatin‐based emulsion‐filled gels (EFGs) tend to liquefy and degradation under heat sterilisation. In this study, transglutaminase (TG) cross‐linking gelatin‐based EFGs with high thermal stability and gel strength were prepared. By analysing the rheological properties, thermal stability, structural changes and their underlying mechanisms, the impact of varying cross‐linking time on the thermal stability and gel strength of EFGs was explored. Results showed that enzymatic EFGs exhibited a higher gel strength with a high elastic modulus and low‐frequency dependence along with a prolonged TG cross‐linking time. The thermal denaturation temperature was increased by 21.87 °C after TG cross‐linking for 4 h compared to that of uncross‐linked EFGs. The surface of fully cross‐linked EFGs was smoother, and the surface voids were reduced. As the TG cross‐linking time increased, the inter‐molecular hydrogen bonds were weakened, the covalent bonds were strengthened and the triple helical structure was altered. After full cross‐linking, the original ordered structure of gelatin molecules was destroyed, the formation of crystalline structure was hindered and the interplanar crystal spacing was more tightly. This study provides a facile method for the preparation of gelatin‐based products with high thermal stability and proposes theoretical guidance for its practical application.