The present invention relates to a method for lyophilizing a composition for multiple target nucleic acid sequence amplification reaction and a lyophilizate prepared by the method. The present method is very effective in lyophilizing a composition containing a high concentration of oligonucleotides. The lyophilizates prepared by the present invention exhibits excellent properties in terms of both sensitivity and specificity, equivalent performance capacity to conventional liquid formulation and furthermore remarkable storage stability. Accordingly, the lyophilizates prepared by the present invention would be very useful in diagnosis.