Recent research underscores the significant impact of digital transformation on innovation and organisational design. However, the specific effect of digital transformation on internal innovation structures within firms remains to be determined. This gap limits our understanding of whether and how digital transformation can redistribute innovation decision-making power. To address this, we investigate the relationship between digital transformation and formal and informal innovation structures. Analyzing a dataset of 26,014 patent applications from 156 listed companies in China's core digital economy industries, our study finds that digital transformation reduces the centralisation of formal and informal innovation structures, with R&D intensity positively moderating this relationship. Additionally, this study reveals that external scientific knowledge amplifies the negative impact of digital transformation on the centralization of informal innovation structure, while external practical knowledge mitigates this effect in formal innovation structure. These findings contribute new theoretical insights to digital transformation and innovation management.