With the rapid development of the digital economy, Internet technology has penetrated into the traditional economic field and has an important impact on the upgrading of the manufacturing value chain. In view of this, the theoretical mechanism of the digital economy affecting the upgrading of the manufacturing value chain is expounded, and an econometric model is further constructed to test. The study found that the digital economy has a significant role in promoting the upgrading of the global value chain of the manufacturing industry, and the results of the robustness test still support the above conclusions; in terms of industries, the impact of the digital economy on technology-intensive and capital-intensive manufacturing is more prominent. From the perspective of different regions, the digital economy has a stronger role in promoting the upgrading of the manufacturing value chain in developed countries; from the perspective of the impact mechanism, the digital economy promotes the upgrading of the manufacturing value chain through technological progress and labor productivity improvement. Therefore, it is necessary to strengthen the construction of digital infrastructure, master the core technologies of the digital economy, attach importance to personnel training, and improve the quality and level of labor in order to realize the upgrading of China's manufacturing value chain.