Alicyclobacillus acidoterrestris (AAT) is a spore-forming bacterium that can survive thermal pasteurization and acidic conditions. Ultraviolet light emitting diode (UVLED) has received extensive attention as a new technology to replace traditional mercury lamps for fruit juice decontamination, however, very few studies on fruit juice have been reported to investigate the sporicidal effect of UVLED on A. acidoterrestris. This research investigated for the first time the application of UVLEDs at 254 nm for the treatment of AAT in tomato juice. The optimized conditions for UVLED, achieved with the aid of Box Behnken design, were 6 cm, 12 min, and 250 mL/min. The results showed that the AAT spores in citrate buffer solution and tomato juice were inactivated by 3-log reduction with a required fluence of 53.67 mJ/cm2. Additionally, UVLED induced an exclusively cellular damage through direct absorption of UV light and direct DNA damage, and indirectly via reactive oxygen species. Besides, the deactivation of AAT spores, validated by LF-NMR analysis, indicated that the free water in AAT might be due to the rehydration of the spore core by the process of germination and then dehydration. This dehydration was further confirmed by the shrinking of spores observed through SEM and AFM imaging. These outcomes were also correlated with those of potassium ions and DPA leakage. This study emphasizes the energy-saving and resistance-reducing features of UVLED in effectively inactivating AAT.