The present invention relates to a composition for stabilizing a fusion protein of a physiologically active protein and an Fc domain, and more particularly to a method of stabilizing a fusion protein of a protein and an Fc domain using a composition containing an ammonium salt or a combination of an ammonium salt and succinate. The composition containing an ammonium salt or a combination of an ammonium salt and succinate according to the present invention can effectively inhibit the aggregation of the protein-Fc domain fusion protein, and thus enables the fusion protein to be stored for a long period of time. Accordingly, the composition can be widely used in the medical field that uses the protein-Fc domain fusion protein.