Encouraging rural innovation and entrepreneurship development and fully stimulating the vitality of rural innovation and entrepreneurship will provide sufficient internal driving force for promoting high-quality development of the county economy. Starting from the perspective of new qualitative factor agglomeration, based on Schumpeter’s entrepreneur theory and Romer’s endogenous growth theory, rural innovation and entrepreneurship were regarded as an organic integration of the whole, and a theoretical framework of “rural innovation and entrepreneurship-new qualitative factor agglomeration-high-quality development of the county economy” was constructed, and the balanced panel data of 1569 counties in China from 2014 to 2021 were used for testing. The results show that the benchmark regression results confirm that rural innovation and entrepreneurship have a significant role in promoting high-quality development of the county economy. The mechanism test finds that rural innovation and entrepreneurship mainly promote high-quality development of the county economy by attracting high-quality labor factor agglomeration, digital factor agglomeration, and intelligent factor agglomeration. New infrastructure construction and financial service level can play a positive regulatory role. Heterogeneity discussion finds that this effect is more significant in the central and western regions, national innovative counties (cities) and regions with strong government support. Therefore, it is necessary to continue to increase support for high-quality development of rural innovation and entrepreneurship, adhere to the focus on attracting and cultivating high-quality labor, improving digitalization level, and intelligence level. Accelerate new infrastructure and financial services, promote the integration of “digital and real” and other external environments, and consolidate the foundation for achieving high-quality development.