With the rise of a new round of technological revolution and industrial transformation, technological innovation has become a central focus in the development strategies of major countries. In this context, big data, as a key factor of production in the digital economy era, urgently requires in-depth exploration regarding its mechanism for promoting high-quality economic development through enhancing regional innovation capabilities. Based on panel data from 281 Chinese cities from 2007 to 2021 and using the establishment of national big data comprehensive pilot zones as a quasi-natural experiment, this paper empirically examines the impact of these pilot zones on regional innovation capabilities and their underlying mechanisms. The findings are as follows. First, the establishment of big data comprehensive pilot zones significantly enhances regional innovation capabilities, a conclusion remaining valid after multiple robustness tests. The spatial Durbin model further reveals that the policy exhibits significant positive spatial spillover effects, with its stimulating effect on the innovation capabilities of neighboring regions even surpassing the local effect, highlighting the innovative spillover value of cross-regional data flow. Second, mechanism tests indicate that the establishment of big data comprehensive pilot zones primarily improves regional innovation capabilities through increasing the number of innovation entities, agglomerating innovation resources, and optimizing the innovation environment. Third, heterogeneity analysis shows that the innovation-enhancing effect of big data comprehensive pilot zones is more pronounced in regions with higher levels of digital economic development, higher marketization levels, and in eastern China. Moderating effect analysis further reveals that strengthening intellectual property protection amplifies the positive impact of big data comprehensive pilot zones on regional innovation capabilities.