The invention provides a method for purifying a compound interferon, which comprises the following steps: adding buffer D to the compound interferon obtained by denaturing the inclusion bodies fermented and collected by conventional methods, adding buffer D while stirring, and then adding the compound interferon that can permeate the molecular weight below 50000 In the dialysis bag, dialyze in the buffer E to carry out the renaturation of the complex interferon protein; separate the supernatant, and use buffer F and buffer G gradient elution on the chromatographic column equipped with strong cation exchange medium, Obtain purified compound interferon. The method can not only completely remove impurity proteins with a molecular weight of 30,000 to 40,000, but also basically separate the refolded intermediates from the fully refolded proteins, so that the obtained compound interferon has high purity and a more uniform product structure.