Scandium, a pivotal metal with widespread applications, faces challenges in recovery due to its highly dispersed distribution. Biological molecules such as proteins and peptides have shown great potential in the field of metal recovery due to their unparalleled affinity and remarkable selectivity. This research aims to design a scandium-binding peptide by mutating the amino acids and optimizing the structure of the EF-hand peptide derived from lanmodulin, a naturally lanthanides-binding protein. Utilizing computer-aided techniques, three peptides-P1 and its two variants (P2 and P3), were screened and synthesized to characterize their interaction with scandium and other competing metals through circular dichroism (CD), atomic force microscopy (AFM), fourier transform infrared spectroscopy (FTIR) as well as column adsorption experiments. Results showed that the peptide P2 and P3 exhibited higher affinity to scandium than P1, as a result of the more binding sites and the existence of hydrogen bonds in the peptides. Moreover, scandium could induce the significant change in backbone structure of these peptides, and coordinated with carboxyl groups of aspartic acid and glutamic acid. The column adsorption experiments with immobilized peptide P3 on microbeads revealed that a final scandium purity of 96.71 % was achieved and a enrichment coefficient of > 103 was obtained. This study offers a transformative strategy for selective scandium extraction from complex industrial matrices and lays the foundation for future innovations in green extraction technologies.