Focusing on 50 representative Chinese cities and applying the ecosystem theory of the business environment, this study employs the fuzzy set qualitative comparative analysis (fsQCA) method to detect the synergistic mechanisms through which the business environment ecosystem of cities affects the manufacturing upgrading. The findings show: First, none of elements in the business environment ecosystem alone could constitute the necessary condition for high manufacturing upgrading. Second, there are three paths for the configuration of high-level manufacturing upgrading, which can be summarized into two modes: “public & innovation” driven mode, and “public & market” driven mode. Third, there are six paths in the configuration of low-level manufacturing upgrading, which can be summarized into three modes: “government & innovation” restricted mode, “human & market” restricted mode, and “government & high rule of law” restricted mode. Furthermore, there is an asymmetrical relationship with the configurations of high manufacturing upgrading performance. Finally, under certain conditions, there are substitutive relationships between elements in the business environment. Overall, this work contributes to the literature on the synergistic mechanisms of business environment ecosystems, and provides practical information for manufacturing firms pursuing upgrading from multiple paths.