Both fish gelatins and mammalian gelatins have been explored in the preparation and application of fish oil-loaded emulsion. However, the comprehensive comparisons and relationships of the structural, functional, and emulsions stability differences between these two gelatins remain unclear. In this work, structural, functional, and the emulsion application differences between commercial cold-water fish skin gelatin (CFG) and bovine bone gelatin (BBG) are explored. The results demonstrated the BBG-stabilized emulsion was more stable than the CFG-stabilized emulsion at 4 °C and higher temperatures (23 °C and 37 °C) decreased the creaming stability differences. The creaming index differences between CFG-stabilized and BBG-stabilized emulsions were mainly dependent on emulsion droplet size and interfacial layer thickness consisted of gelatins. Further, the possible reason for CFG's lower emulsion stability at 4 °C might be mainly dependent on its higher β-antiparallel percentage in the secondary structures and its lower thickness of gelatin film-like nanostructures. This work will provide useful information to understand the relationship between structure and function of protein. It also will provide a guide for the application of fish oil-loaded gelatin-stabilized emulsions in food beverages and other foods such as surimi.