Wicked problems have emerged as a focal point in policy research, with project-based governance representing a conventional approach to address these issues. Taking the defense of blue sky and clear water in H province as case study, this paper tries to reveal the logic of policy implementation in the project-based governance for wicked problems, and analyzes the generative mechanisms of “compliance-adaptation” implementation, so as to explain how the project system fosters effective governance of such challenges. Through a multi-case analysis, we discover that the project system enhances constraints on means and processes during policy implementation. The interaction between project goals and policy objectives facilitates a two-stage implementation process. We categorize“compliance-adaptation” implementation into four types based on the variables of tool suitability and resource adequacy. The double-edged sword effect, along with institutional arrangements, elucidates the generative mechanisms of “compliance-adaptation” implementation. While the project system addresses dilemmas associated with wicked problems—such as insufficient information, resources, and motivation—it also introduces challenges like adaptability risks, project fragmentation, and structural resource shortages, which may undermine the overall effectiveness of governance. Effective adaptive implementation, aimed at achieving policy objectives, relies on specific institutional arrangements. The “compliance-adaptation” implementation reveals the complexity theory implication within the project-based governance for wicked problems.