A cross-linked (CL) collagen peptide (CP)-potato starch (PS) compound (CL-CP-PS) was prepared by autoclaving PS and CP and subsequently cross-linking with a microbial transglutaminase (MTGase). CP-compounded PS (CP-PS) was prepared by autoclaving a mixture of PS and CP at 120°C for 120 min. After suspending in an MTGase solution, CP-PS was cross-linked with MTGase at room temperature for 24 h while shaking. The reaction product was washed three times with distilled water, and then air-dried to obtain CL-CP-PS. CL-CP-PS showed a clear polarized image almost the same as that of PS, and had a 0.7% CP content. The median diameter of CL-CP-PS was significantly larger than that of CP-PS or of PS, suggesting the formation of multiple granules through cross-linking among the compounded CP moieties. CL-CP-PS exhibited a grater thermal structural stability, lower swelling index and solubility, as well as higher heat resistance for maintaining the swollen starch granules at 120°C for 20 min than those of CP-PS and PS. Cross-linking of CP-PS with MTGase should thus be valuable for providing a starch material having high rigidity, low swelling index and solubility, and enhanced heat resistance.