OBJECTIVE To establish and verify a ddPCR method to determinate the proportion of mRNA components in multivalent mutant COVID-19 mRNA vaccine. METHODS Different types of coronavirus mRNA were used as target genes, and their conserved sequences were selected to design primers and probes. The ddPCR method for measuring the proportion of multivalent mutant COVID-19 mRNA vaccine components was established, and the linear range, repeatability, accuracy, intermediate precision, durability and applicability of the method were verified. RESULTS When the total mRNA concentration ranged from 1 to 150 pg·mL-1, the linearity was good. Repeatability coefficient of variation(CV) was within 10%. The recoveries of accuracy verification were 84%-114%, CV＜10%. The intermediate precision and durability coefficient of variation CV were all＜ 5%, and the CV of the proportion of components in the four different bivalent COVID-19 mRNA vaccines was all≤5%. CONCLUSION The ddPCR method established for detecting the component proportion of multivalent mutant COVID-19 mRNA vaccine has high sensitivity, good stability and strong specificity, which is suitable for detecting the component proportion and content of multivalent COVID-19 mRNA vaccine.