In order to conform to the development trend of the digital age, China has established the strategy of “digital China” to build a new competitive advantage. Data element has become the fifth production element in addition to labor, capital, land, and technology. With the acceleration of data elements and the formation of data element market, it has injected strong impetus into the digital economy and scientific and technological innovation. Data element agglomeration leads technology flow, capital flow, and talent flow with data flow, and promotes the agglomeration of innovation elements such as high-tech enterprises, R&D capital, and technical talents, which not only facilitates the acquisition and integration of innovation resources for enterprises, but also improves R&D input and innovation output. To give full play to the role of data elements in structural optimization, model innovation, and institutional reform, it is urgent to clarify the influence mechanism of data element agglomeration on scientific and technological innovation. Using 30 provinces in China from 2001 to 2019 as the research sample, this paper takes the construction of Big Data Comprehensive Pilot Areas as a quasi-natural experiment, and uses the DID fixed-effect model to investigate the impact of data element agglomeration on the construction of innovation highland. It is found that data element agglomeration significantly promotes the construction of innovation highland in pilot areas, and this conclusion has strong robustness after PSM-DID and placebo tests. Taking topographic relief as the instrumental variable of data element agglomeration, it is found that the impact of data element agglomeration on the construction of innovation highland is still positive when the endogenous problem is fully considered. The results on the influence mechanism show that data element agglomeration has a positive impact on the construction of innovation highland by alleviating the mismatch of labor resources and improving the level of R&D expenditure and human capital. The expansion analysis shows that data element agglomeration has an obvious spillover effect, and data element agglomeration in a region can carry out positive spillover to the surrounding areas, thus improving the construction of innovation highland in the surrounding areas. Heterogeneity analysis shows that the policy effect of data element agglomeration is more obvious in regions with a higher level of digital infrastructure, marketization degree, and digital economy development. Therefore, we should actively promote the gradient expansion of Big Data Comprehensive Pilot Areas, promote the opening of data elements and the application of big data integration, and better release the dividends of data element agglomeration.