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.
