Green innovation is an important force to improve the quality and efficiency of regional economy. How to promote green innovation and improve urban green competitiveness is an important issue to be answered in the field of innovation. This paper, integrating the transaction cost theory, the knowledge spillover theory, and the resource allocation theory, analyzes the data of 254 prefecture-level and above cities by using qualitative comparative analysis (QCA), non-compartmental analysis (NCA), and propensity score matching (PSM), and by exploring the linkage effect of heterogeneous environmental policies, institutional environment, and agglomeration effect on urban green innovation from the overall perspective, as well as whether different green innovation paths are conducive to the improvement of urban green competitiveness. The results show that a single antecedent does not constitute a necessary condition for the generation of high green innovation, nor does it constitute a sufficient condition for the generation of high green innovation. Heterogeneous environmental regulation, institutional environment, and agglomeration effect are linked and matched, forming a diversified configuration form of urban green innovation, with obvious characteristics of “different paths leading to the same destination”. It is embodied in the institutional environment-oriented model, the command-and-control oriented-model, the market incentive-oriented model, and the policy combination-oriented model. There are significant differences in the impact of the four green innovation models on urban competitiveness, with the characteristics of “different ways leading to different effects”, and the impact of different green innovation modes on urban competitiveness has a hysteretic effect. The research conclusion reached in this paper provides a decision-making basis for cities to conduct green innovation and enhance competitiveness from the perspective of configuration, compensate for the limitations of traditional quantitative analysis on this issue, and enriche the green innovation theory to a certain extent.