The digital economy, with data as its key production factor, has been leading a high quality development. The digit-oriented transformation of substantial economy has been shifting towards the functioning model of digital economy.The linkage mechanisms to integrate digital economy and substantial economy have been probed into, that is, the digit-oriented transformation of traditional physical industries expands the development space for digital economy and at the same time the development of digital economy promotes traditional physical industries in its platform, network, digital operation and efficiency improvement. The development of digital economy has given rise to the demand for a huge and new market, has stimulated further development of substantial economy, has slowed down the constraints of space on economic activities, and has expanded the spatial scope for resource allocation, and in turn substantial economy has realized the data-driven resources allocation in digital space in actual geographic space, which demonstrates that both digital economy and substantial economy are mutually complementary. This study not only enriches the research on their deep mutual integration mechanisms, but also expands the research on the operation mode of digital economy, providing theoretical enlightenment for the promotion of digital China strategy.