This study aimed to investigate the effect of phosphorylation on the structure and emulsification of Coregonus peled, Esox lucius and Grass carp scale gelatin. Fourier transform infrared spectroscopy (FTIR) and endogenous fluorescence spectra showed that the structures of the three fish scale gelatins changed. Additionally, the surface hydrophobicity index of the three fish scale gelatins increased by 36.72, 31.42 and 111.67, respectively, after 1 h of phosphorylation, and the surface tension decreased by 17.27, 32.58 and 18.7 mN/m, respectively. The emulsification activity index increased by 115.86, 155.22 and 45.52 m2/g, and the emulsification stability index increased by 98.37, 256.77 and 169.61 min, respectively. The structure of fish scale gelatin changed after phosphorylation, which resulted in the improvement of emulsification. This work will provide useful information to understand the relationship between the structure and function of gelatin.