The present invention relates to a method for preparing a TNFR-Fc fusion protein mixture containing a target content of hydrophobic chromatogram peak 3, and to a method for adjusting the content of hydrophobic chromatogram peak 3 and, specifically, to a method for preparing a TNFR-Fc fusion protein mixture using a hydrophobic chromatograph medium containing an aromatic functional group, which is pre-equilibrating with an equilibration buffer comprising sodium chloride or ammonium sulfate, on a sample comprising a TNFR-Fc fusion protein mixture liquid produced from mammal cells, and to a method for adjusting the content of hydrophobic chromatogram peak 3 by hydrophobic chromatography using an equilibration buffer containing a predetermined concentration of sodium chloride or ammonium sulfate. The present invention can provide a method for producing a TNFR-Fc fusion protein by, in the production of the TNFR-Fc fusion protein using hydrophobic chromatography, performing hydrophobic chromatography through the equilibration using an equilibration buffer containing a predetermined concentration of sodium chloride or ammonium sulfate, thereby adjusting the content of hydrophobic chromatogram peak 3 to contain a target content of hydrophobic chromatogram peak 3. Therefore, the method presented above can be favorably used in the manufacturing of biological medicines comprising a recombinant protein, such as etanercept produced from animal cell culture through genetic recombinant technology.