Molecular modification has attracted many attentions in the field of gelatin science. In this work, a transglutaminase (TG) modification method was developed and applied to modify bovine bone gelatin, porcine skin gelatin, and cold-water fish skin gelatin, and then the effect of TG crosslinking on the structural, physicochemical, functional, and emulsion stabilization properties of three types of gelatins were explored and compared. The results demonstrated that TG modification increased the nanoparticle formation behaviors and change the physicochemical and functional properties of three types of gelatins. Further, TG-modified aquatic gelatin showed comparable foaming properties (147% ± 6% for foaming capability and 55% ± 4% for foam stability) and higher emulsifying properties (18 ± 1 m2/g for emulsion activity index and 142 ± 11 min for emulsion stability index) to unmodified mammalian gelatins. In addition, TG-modified gelatins decreased the droplet sizes and increased creaming stability of fish oil-loaded emulsions compared with unmodified gelatins. All these results suggested TG modification was an efficient molecular modification method for gelatins. Moreover, TG-modified aquatic gelatin could be potential mammalian gelatin replacer. This work could provide useful information to understand the relationship among animal sources, tissue sources, extraction methods, amino acid compositions, molecular modification, molecular structure, physicochemical properties, functional properties, and emulsification stability of gelatins.