The digital economy is the future direction of global development, and its innovation-driven effect has become the focus of scholars. This study takes China’s Shanghai and Shenzhen A-share listed manufacturing enterprises from 2012 to 2022 as research samples and uses a text-analysis method to measure the comprehensive index of the regional digital economy. Based on the dual dimensions of quantity and quality, we empirically test the actual impact of the digital economy on manufacturing innovation. The results show the following: (1) The internal components of the digital economy include data elements, digital technology, and digital infrastructure, which have a significant role in promoting manufacturing innovation. (2) There are significant differences in the release of digital economy innovation dividends among enterprises with different growth stages, property rights, and technology endowments. (3) From the macro-regional level, the rational allocation of R&D personnel and R&D funds is an effective way for the digital economy to enable manufacturing innovation. In addition, from the micro-enterprise level, factor-combination and information-optimization effects are also effective ways for the digital economy to drive manufacturing innovation. (4) Further, the impact of the digital economy on manufacturing innovation is nonlinear, with changes in internal composition. This study helps to break through the obstacles of the digital economy to achieve innovation empowerment and provides a theoretical reference for the manufacturing industry to continue to spur innovation vitality.