Under the global digital transformation, the integration of digital economy and real economy(IDR) is the key to promoting high-quality economic development. The establishment of the big data comprehensive pilot zones, as a major policy initiative in the big data field, has not been adequately examined for its impact on the IDR. Panel data from Chinese cities between 2011 and 2021 were utilized. The entropy-weighted TOPSIS method and a coupling coordination model were employed to measure the level of IDR across 227 cities. A staggered difference-in-differences model and a mediation effect model were applied to verify the promoting effect of the pilot zones on the IDR and to analyze its underlying mechanisms. Multiple robustness tests were conducted, with differential effects examined across city sizes, geographic locations, and establishment batches. The findings show that the construction of big data comprehensive pilot zones enhances the IDR, with effects strengthening over time. The promotion is more pronounced in medium-sized and larger cities, coastal cities, and among the second batch of the big data comprehensive pilot zones. The mechanisms involve the stimulation of technological innovation, increased entrepreneurial activity, and advancement of industrial structure upgrading. The policy effectiveness of the big data comprehensive pilot zones in fostering the IDR is highlighted, and the mechanisms which they operate are clarified. Empirical evidence from Chinese cities is provided, contributing to the understanding of big data policy impacts and factors influencing the IDR, to some extent alleviates the problem of insufficient attention to the IDR of the prefecture-level administrative regions in existing research and offers a new theoretical perspective on how big data policies can promote the IDR.