Regional science and technology innovation capacity is an important starting point for leading high-quality development. Building regional science and technology innovation centers is conducive to gathering innovation elements and resources and promoting the improvement of the capabilities of various innovation entities. At the same time, in order to accelerate the strategic deployment of big data and create an innovation landscape led by big data, as a data element distribution center and a big data industry gathering place, the big data comprehensive pilot zone can provide data sharing dividends and industries for regional technological innovation development. It supports the engine and contributes to continuous practice and sums up big data industry development experience that can be promoted and replicated across the country. Based on the quasi-natural experiment established in the big data comprehensive pilot zone, this study adopted a multi-period double difference (DID) model to conduct statistical analysis on panel data of 30 provinces (including municipalities and autonomous regions) from 2011 to 2021, in order to explore the impact of the big data comprehensive pilot zone on regional science and technology innovation capacity and the implementation effects of different pilot policies. Research results show that the establishment of a national big data comprehensive pilot zone has significantly improved regional science and technology innovation capacity. This conclusion still holds true after passing the placebo test, lag one-period model and robustness test excluding first-tier cities. In order to further explore the effect of different pilots in the national big data comprehensive pilot zone on the science and technology innovation capacity of surrounding areas, this article also conducted a heterogeneity analysis on the eight pilot areas. The results show that, firstly, the policy effects of the eight major pilots are different, that is, different pilots in the national big data comprehensive pilot zone have different effects on the science and technology innovation capacity of surrounding areas, with spatial and regional differences. Second, the heterogeneity analysis results of the national big data comprehensive pilot zones in Guizhou, Beijing-Tianjin-Hebei, Henan, Inner Mongolia, and Shenyang are significantly positive, indicating that the big data comprehensive pilot zone policy has a significant effect on the regional science and technology innovation capacity of these pilots. Third, the heterogeneity analysis results of the national big data comprehensive pilot zones in Shanghai, the Pearl River Delta, and Chongqing are not significant, indicating that the policy effect of the big data comprehensive pilot zones is not obvious in these areas. This article further explores the reasons for this result, which are attributed to differences in local economic development foundations, policy implementation goals, and innovation distribution structures. Based on this, corresponding policy suggestions are put forward. On the one hand, it is recommended to strengthen inter-regional policy coordination and promote the exchange, sharing and integration of innovative resources between regions. On the other hand, for the Pearl River Delta, Shanghai, and Chongqing pilot areas, policy implementation should consider based on the actual development of local science and technology innovation, we will further optimize the adaptability of big data pilot zone policies, ensure the precise implementation of policies, and promote the coordinated development of regional science and technology innovation capacity.