Promoting high-quality development of county-level economies and accelerating the high-quality integration of urban and rural areas serve as crucial levers for constructing a new development paradigm. Innovation-driven development, by enhancing innovation levels within counties, can strengthen the endogenous growth momentum of county economies. However, existing literature remains insufficient in examining how innovation, viewed through the lens of innovation policy, elevates the development level of county economies, particularly lacking research on how macro-level innovation policies enhance county economic development. Based on the county-level panel data from 2012 to 2022, this paper uses the exogenous policy shock of the construction of the first batch of national innovative counties and adopts the PSM-DID method to systematically evaluate the impact of the implementation of the national innovative county policy on county-level economic development. The research results show that the construction of national innovative counties has a significant promoting effect on county-level economic development, and this effect still holds after a series of robustness tests. The mechanism test indicates that the construction of national innovative counties promotes county-level economic development by improving the county-level innovation level. The heterogeneity analysis reveals that in counties with low entrepreneurship levels, low industrialization levels, and low economic development levels, the construction of national innovative counties has a stronger promoting effect on their economic development, which reflects the regional balanced development effect of the policy. The moderating effect test shows that the marketization level and the digital technology level can positively moderate the promoting effect of the policy on county-level economic development. Compared with previous studies, this paper makes expansions in the following two aspects. Firstly, it enriches research on evaluating national-level innovative county policies. By using the Difference-in-Differences (DID) method combined with Propensity Score Matching (PSM), this paper systematically identifies the net effect of the construction of national innovative counties on county-level economic development, and further reveals the internal mechanism, heterogeneity characteristics, and endowment adjustment effect of the policy. Second, it broadens the research perspective on the innovation-driven development of county-level economies. By integrating the state-led institutionalized innovation system of innovative county development into the analytical framework for county-level economic growth, this study constructs a theoretical framework and employs empirical analysis to reveal the structural impact of macro-level innovation policies on county-level economic systems. This provides fresh insights into understanding the synergistic role of government and market forces in county-level innovation. This study, to a certain extent, reveals the intrinsic logic linking the development of national-level innovative counties with county-level economic growth. It assists government departments in enhancing endogenous development momentum within counties under the “innovation-driven development” strategy, thereby fostering the sustained advancement of county innovation alongside coordinated county-level economic development and elevating regional coordination levels. Additionally, the findings provide empirical evidence for further optimizing the implementation pathways of national-level innovative county policies, holding significant practical implications for promoting the formation of a new county-level economic development paradigm driven by innovation.