Most commentators understand that contemporary social, economic and environmental challenges require quality governance from global to local scales. While public scrutiny of governance has increased in recent years, the literature on frameworks and methods for analysis in complex, poly-centric and multi-thematic governance systems remains fragmented; displaying many disciplinary or sectoral biases. This paper establishes a stronger theory-based foundation for the analysis of complex governance systems. It also develops a clear analytical framework applicable across a vast array of differing governance themes, domains and scales (GSA). The key methodological steps and evaluative criteria for the GSA framework are determined and practical guidance for its application in reform is provided.