The present invention is to provide a two-stage sterilization process for treating heat-resistant spores in a great burdock extract drink, which comprises the steps of sealing dried great burdock and water in a double-kettle pressure cooker; heating liquid mixture of great burdock and water to a first temperature range lower than or equal to 100° C. for at least a first duration during a first-stage sterilization; opening lid of the cooker and filtering out great burdock residue so that all that remains in the cooker is great burdock extract; resealing the cooker and heating the great burdock extract to a second temperature range higher than or equal to 120° C. for at least a second duration during a second-stage sterilization, and the pressure in the cooker during the second-stage sterilization is higher than that during the first-stage sterilization; so as to obtain the extract drink free of common bacteria and heat-resistant spores.
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