In recent years, the global booming of the digital economy has become a booster for China’s high-quality development. In the digital economy era, the digital upgrading of the industrial structure has become obvious. Based on a grey relational entropy model and dissipative structure theory, our empirical study reveals that the impact of the digital economy on the industrial structure varies over time. Since 2013, the digital economy has become an engine for China’s continuous industrial structure upgrading. By comparing the influence of the development of digital industrialization and the industrial digitization on industrial structure upgrading, we find that the former has a foundational leading role in the upgrading of the industrial structure, but the latter has a stronger impact. Therefore, the digital economy is an important driving force being able to lead the future upgrading of the industrial structure. China should rapidly promote the construction of new digital infrastructure and implement strategic spatial layouts for the development of digital industrialization while concurrently accelerating the industrial digitization. This will enable China’s economy to achieve higher-quality, more efficient and more secure development in the post-epidemic era. It is also an effective means for accelerating the development of a modern industrial system and will promote the upgrading of the economy.