Regional coordinated development is a crucial aspect of China’s regional economics and an important manifestation of Chinese-style modernization. Industries serve as the primary vehicle for achieving this goal, and in the era of digital economy, industrial development must be guided by data and information. The Third Plenary Session of the 20th Central Committee of the Communist Party of China proposed improving the institutional mechanisms for deep integration between the real economy and the digital economy, as well as enhancing the strategic mechanisms for regional coordinated development. The 2024 Central Economic Work Conference explicitly called for actively applying digital and green technologies to transform and upgrade traditional industries, while enhancing the innovation capabilities and radiating effects of economically advantaged regions. Based on the reality that China’s four major regions are at different stages of development, this study uses the entropy method to conduct an empirical analysis of factor innovation, industrial digitization, and regional coordinated development levels across 31 provinces (municipalities and autonomous regions) from 2003 to 2023. Given that China’s digital economy entered a mature phase starting in 2013, factor innovation is taken as the explanatory variable, regional coordinated development level as the explained variable, and industrial digitization as the mediating variable. High-quality talents, regional economic foundations, urban-rural disparities, and government support are identified as control variables. A difference-in-differences approach is employed to analyze the relationships among these three factors from 2013 to 2023. The findings reveal that: 1) Factor innovation, industrial digitization, and regional coordinated development have reached relatively high levels in major urban agglomerations such as Beijing-Tianjin-Hebei, the Yangtze River Delta, the Pearl River Delta, Shandong Peninsula, Central Plains, the Middle Reaches of the Yangtze River, and Chengdu-Chongqing, with industrial chains serving as the link for inter-agglomeration industrial division. 2) Technological innovation drives the development of new quality productivity, but industries dominated by traditional production factors still account for a significant proportion. 3) There is a structural imbalance between the supply of high-quality talent and the demand for industrial digitization, particularly constraining the digitization of the secondary industry. 4) Government support exhibits mismatches in promoting industrial digitization through factor innovation to advance regional coordinated development, thereby affecting the effectiveness of a proactive government in guiding the construction of an efficient market. 5) Considering both the east-west and north-south dimensions, a virtuous cycle of factor innovation, industrial digitization, and regional coordinated development has formed in North China, Central China, South China, and East China, where modern industrial systems are relatively well-developed, while other regions lag behind. Based on these findings, this paper proposes corresponding countermeasures: leveraging a proactive government to guide an efficient market; solidifying the foundation for factor innovation to drive industrial digitization and promote regional coordinated development; innovating human capital cultivation and development mechanisms to address structural talent gaps in implementing innovation-driven strategies; expanding technological innovation to cover the modern industrial system to comprehensively develop new quality productivity; and fully utilizing the advantages of the digital economy and industrial chains to refine industrial division and deepen industrial cooperation across the eastern, central, western, and northeastern regions.