A microbial transglutaminase (TGase) was used in this work as biocatalyst to prepare a cross-linked casein–gelatin composite, a modified protein product with 4-hydroxyproline about 41 mg g−1 peptides. Some cross-linking conditions such as total protein content, the ratio of caseinate to gelatin and original pH were fixed at 5% (w/v), 4:1 (w/w) and 7.5, respectively. Other suitable conditions selected by single factor trials were TGase addition of 20 U g−1 peptides, reaction temperature of 45 °C and reaction time of 4 h. Peptide profiles from SDS-PAGE analysis showed the composite was peptide polymers. Compared to that of the original caseinate or the cross-linked caseinate, the dispersion of the composite exhibited a markedly enhanced apparent viscosity, storage modulus and viscous modulus. Meanwhile, the composite also showed a better water holding capacity, unchanged oil binding capacity and lower enzymatic digestibility in vitro, conferring its applicability as a new protein ingredient.