Accelerating the construction of eco-environmental big data governance platform, promoting the coordinated progress of Digital China construction and green development, are the key driving forces to improve the ecological civilization system, realize the intelligent escort of green water and green mountains. Based on panel data samples of Chinese listed companies, this paper takes the implementation of the Construction Plan of Eco-environmental Environment Monitoring Network as a quasi natural experiment, and uses the Difference-in-Difference method to examine the impact of eco-environmental big data governance policy on enterprise green innovation. The research finds that: (1)eco-environmental big data governance has promoted the enterprises with environmental risk to increase green innovation, which is achieved by overcoming the shortage of the environmental protection institutions staff, increasing the severity of environmental penalties, enhancing enterprises’ green awareness and increasing environmental expenditure.(2)With the improvement of regional environmental monitoring equipment and network facilities, eco-environmental big data governance can better promote the increase of enterprises’ green invention patent applications. (3)The perfection of informatization laws, dynamic monitoring and joint defense system are the key to promoting the precision of environmental big data governance and supporting green substantive innovation. Faced with more complex environmental governance issues in the new era, the thorough analysis on the impact of eco-environmental protection big data governance on green innovation and its internal mechanism, can provide new for China to build empirical evidence the modern environmental governance system and promote the development of new quality productivity, which is an expansion and supplement for existing theories.