In this study, microbial transglutaminase (MTGase) and pectin were compared to modify bighead carp (Hypophthalmichthys nobilis) scale gelatin. The functional properties of modified fish scales gelatin (FSG) were largely improved, including melting temperature and rheological behavior. While, modification methods decreased the triple-helix content and destroyed the single left-hand helix chain of modified FSG as investigated by X-ray diffraction. MTGase could induce the denser and finer gels network, but had none significant effect on nanostructural properties of fish gelatin. Pectin inserted itself into the fish gelatin gels network and caused aggregations, forming crystalline peaks and various nanostructures. In particular, compared with pectin modified FSG, MTGase produced FSG with lower storage modulus and apparent viscosity, but higher gel points and melting points.