Naringinase was mainly obtained by microbial fermentation, and mutagenesis was a major way for obtaining excellent mutants. The aim of this study was to screen out a high naringinase yielding mutant to enhance the potential application value of its industrialization and compare the effects of different mutagenic methods on the enzyme activity of the strain. A novel producing naringinase strain, Aspergillus tubingensis MN589840, was isolated from mildewed pomelo peel, later subjected to mutagenesis including UV, ARTP and UV‐ARTP. After five rounds iterative mutagenesis, the mutants U1, A6 and UA13 were screened out with 1448·49, 1848·71, 2475·16 U mg−1 enzyme activity, the naringinase productivity raised by 79·08, 123·56 and 206%, respectively. In addition, the naringinase activity of three mutants rose after each round of iterative mutagenesis. These results indicated that the mutagenesis efficiency of UV‐ARTP was higher than that of single ARTP, and both are better than UV. In summary, the iterative UV‐ARTP mutagenesis is an effective strategy for screening high naringinase‐producing strains. Significance and impact of the study: The ‘delayed bitterness’ of naringin in citrus processing is a challenging problem restricting the development of citrus processing industry. Naringinase can transform naringin to naringenin for debittering. Therefore, it is significant to breed high naringinase‐producing strains suitable for industrialization. In this study, we screened a naringinase high‐yielding mutant, which had potential industrial application value and laid a foundation for the development of citrus processing industry. In addition, the method of iterative UV‐ARTP mutagenesis provided an effective strategy for breeding high‐yield naringinase‐producing mutants.