The gelling and structural properties of microbial transglutaminase (MTGase) and pectin modified fish gelatin were compared to investigate their performances on altering fish gelatin properties. Our results showed that within a certain concentration, both MTGase and pectin had positive effects on the gelation point, melting point, gel strength, textural, and swelling properties of fish gelatin. Particularly, low pectin content (0.5%, w/v) could give fish gelatin gels the highest values of gel strength, melting temperature, and hardness. Meantime, flow behavior results showed that both MTGase and pectin could increase fish gelatin viscosity without changing its fluid characteristic, but the latter gave fish gelatin higher viscosity. Both MTGase and pectin could increase the lightness of fish gelatin gels but decreases its transparency. More importantly, fluorescence and UV absorbance spectra, particle size distribution, and confocal microscopy results indicated that MTGase and pectin could change the structure of fish gelatin with the formation of large aggregates. Compared with MTGae modified fish gelatin, pectin could endow fish gelatin had similar gel strength, thermal and textural properties to pig skin gelatin.