The invention relates to a production method of high fructose corn syrup without alicyclobacillus acidoter-restris. Starch milk is subjected to a series of treatment such as high-concentration liquefaction, saccharification, isomerization, chromatography, refining, membrane filtration, sterilization filtration, concentration and the like, and orderly cleaning and disinfection measures are taken for all procedures in the production process, so that the final production of the high fructose corn syrup product without alicyclobacillus acidoter-restris is ensured. The method has the advantages that: the high-concentration liquefaction is adopted for liquefaction, so that a certain bacteriostatic effect and an energy-saving effect are achieved; in order to ensure the introduction risk of alicyclobacillus acidoter-restris of source feed liquid, the high-temperature sterilization is carried out at a spray liquefaction temperature of 125-148 DEG C in the liquefaction process; and in addition,certain disinfection measures are made for isomerization and chromatography processes in the production process, so that alicyclobacillus acidoter-restris is prevented from breeding in the productionprocess, and the dead corner for alicyclobacillus acidoter-restris breeding is avoided as much as possible in the production process. The process is simple, convenient and feasible, facilitates industrial production control, and improves the quality of high fructose corn syrup products.