County-level innovation capability is a key link in promoting the deepening development of the national innovation system. Although there has been extensive research on the factors that affect county-level innovation capabilities, most studies have a mismatch between theory and methods. In theory, it is most appropriate to explain the reasons for improving county-level innovation capabilities from the perspective of complex systems. However, research methods lack the ability to capture the complex interactive effects between various conditions that affect innovation capability. In addition, it is necessary to seek new explanatory perspectives for the many conflicting findings in the literature. This study is based on the theories of complex systems and regional innovation systems, utilizing relevant data from 52 counties in Zhejiang, China, and using the fsQCA method from a holistic configuration perspective to study the multiple paths and mechanisms that promote synergy between the government and the effective market, attract factors to "reverse flow," and drive the improvement of county innovation capabilities. Research has found that a single factor is not a necessary condition to enhance the high county innovation capacity. The configuration that generates high county innovation capabilities can be summarized into four types: the joint driving model of innovative entities and responsible government; the joint driving model of collaborative production factors and responsible government; driven by the traditional industrial upgrading model; and the joint driving model of traditional industrial upgrading and responsible government. The research conclusion also reveals that the business environment plays an important role in the process of enhancing county innovation capabilities, but the innovation main body is the new force in enhancing county innovation capabilities. The various elements that affect the innovation capacity of the county adapt to each other, co-evolve, and evolve into different ecosystems, forming a diversified and differentiated driving path.