Promoting the in-depth integration and positive interaction between data elements and green innovation is conducive to unleashing the ‘multiplier effect’ of data elements and boosting the efficient development of the green economy. Based on the panel data of 283 cities in China from 2011 to 2021, the double-difference method is used to assess the role of data elements in driving the green innovation capacity of cities, taking the national-level big data comprehensive experimental zone as a quasi-natural experiment. It is found that data elements have a significant facilitating effect on urban green innovation, and this conclusion still holds true after the robustness test of multiple methods. The mechanism test shows that data elements empower urban green innovation by optimizing the efficiency of factor allocation, increasing entrepreneurial activity, promoting the development of green finance, and facilitating the upgrading of industrial structure. The heterogeneity test reveals that the positive effect of data elements on green innovation is more pronounced in large cities, highly marketized cities, and regions with greater data openness, robust data governance, and strong data security. The spatial spillover effect test shows that the development of data factors in this city can also enhance the level of green innovation in the neighboring areas, and the distance between cities is 500-700 km as the significant effective area of spatial spillover effect. The research results help to understand the internal logic of the data elements empowering urban green innovation, and provide a powerful reference for promoting the synergistic development of digitization and greening.