The invention mainly relates to a linaclotide purifying method and belongs to the technical field of bioseparation. According to the linaclotide purifying method, an ion exchange chromatography method and a high-performance liquid chromatography method are combined, an anion exchange column is adopted as a stationary phase, a Tris HCl buffering solution is adopted as a mobile phase A, a NaCl-contained Tris-HCl buffering solution is adopted as a mobile phase B, a gradient eluting method is adopted to treat a crude linaclotide solution, eluate is subjected to desalination and acetate changing by means of the high-performance liquid chromatography method, a C18 column is adopted as a separating medium, after a sample is loaded, gradient elution is performed by adopting an aqueous acetic acid solution as the mobile phase A and acetonitrile as the mobile phase B, and eluate is subjected to freeze-drying to obtain pure linaclotide. The linaclotide purifying method is simple to operate, low in separation cost, high in yield and suitable for large-scale linaclotide production; purity of the obtained pure linaclotide can reach to above 99%, so that the obtained pure linaclotide is low in impurity content and has favorable economic and practical values and an extensive application prospect.