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• A simultaneous microwave/ultrasonic-assisted enzymatic extraction method was established for the first time. • Simultaneous microwave/ultrasonic-assisted enzymatic process can improve antioxidant capacity of juice by-product extract. • Simultaneous microwave/ultrasonic-assisted enzymatic process can increase the extraction efficiency of antioxidant ingredients. • <b>Nitraria tangutorun</b> Bobr. juice by-products extract exhibited excellent cell protection effect from oxidative injury.<br>By-products originating from food processing are a considerable disposal problem for the food industry. Because of the absence of specifically effective processing technology, huge quantities of by-products are often abandoned as rubbish and prone to microbial spoilage. Given this, a simultaneous microwave/ultrasonic assisted enzymatic extraction (SMU-AEE) method was established for the first time, and performed for antioxidant ingredients extraction from <b>Nitraria tangutorum</b> juice by-products (NJB) in the present study. Its experimental conditions were optimized by single factor test and response surface methodology (RSM), and gave the corresponding response values for antioxidant capacity of NJB extract (NJBE) of 219.73 ± 7.03 mg TE/g, which was 27.62%-190.23% higher than those obtained by traditional extraction methods. Chemical composition assay suggested that the increasing of antioxidant capacity of NJBE by SMU-AEE was because of the improvement of extraction efficiency of antioxidant ingredients from NJB, including phenols, flavonoids and anthocyanins. Furthermore, oxidative injury protection ability assay showed that NJBE was good at protecting cells from UVB-oxidative phototoxicity and doxorubicin-oxidative cardiotoxicity, and its protecting ability surpasses or approaches to that of grape seed extract (GSE, the positive control drug), indicating its good potential to be a natural antioxidant in food and pharmaceutical industries.