Kiwifruit NFC juice is characterized by high nutritional value; however, quality deterioration is readily induced by conventional thermal sterilization. To compare the effects of EBI and UHT sterilization on the storage quality of kiwifruit NFC juice and to identify the optimal irradiation dose, the juice was treated with EBI at doses of 3, 5, and 7 kGy or with UHT at 115 ℃ for 6–10 s, and subsequently stored at 4 ℃ for 28 days. The microbial safety, sensory and physicochemical characteristics, bioactive components, and aroma quality were systematically evaluated. It was shown that commercial sterility equivalent to that achieved by UHT was obtained by EBI at doses of 5 kGy and above, while pH value, total soluble solids content, and color stability were better maintained. Among all treatments, the highest retention of total phenolics, reducing sugars, and key aroma compounds was observed in the 5 kGy EBI group; specifically, the total phenolic content was decreased by 15.29% in the UHT group and by only 4.73% in the 5 kGy group at the end of storage. Severe loss of fruity aroma was caused by UHT, whereas slight flavor deterioration was induced by the 7 kGy treatment. In conclusion, microorganisms are effectively inactivated by EBI at 5 kGy, and the sensory, nutritional, and flavor quality of kiwifruit NFC juice are maximally maintained; therefore, EBI at 5 kGy is regarded as a preferred non-thermal processing alternative to conventional UHT. A theoretical basis for the industrialization of non-thermal processing technologies in high-end fruit juice production is provided by this study.