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The attainment of regional high-quality development necessitates the critical role of the digital economy in facilitating the transformation of industrial structures. This study intends to investigate the effect of the digital economy on industrial structure transformation from the perspective of innovation factor allocation using a panel dataset of 41 cities in the Yangtze River Delta region for the period from 2011 to 2020. This paper considers four dimensions to measure the level of industrial structure transformation i.e. industrial structure servitization, industrial structure upgradation, service industry structure upgradation and industrial interaction level. The results of the study suggest that the digital economy can significantly improve industrial structure transformation. The results remain consistent even after several robustness checks. Further, the analysis of the mechanism of action shows that the digital economy can promote industrial structure transformation by optimizing the innovation factor allocation. The study provides several policy implications for the digital economy and its role in the promotion of industrial structure transformation.