Designing environmental governance structures and in particular ecosystem services governance structures, means modifying, replacing, or creating institutional arrangements. Several scholars have tried to identify sets of functioning and particularly preferred institutional design principles for environmental governance. Comparative institutional analysis (CIA) plays a major role in this process and refers to comparing real-world institutions, organizations, decision-making structures, and coordination mechanisms. CIA attempts to determine preferred institutional arrangements among several possibilities. Within the paper, it is emphasized that the set-theoretic Qualitative Comparative Analysis (QCA) approach and technique may support CIA. Therefore, different institutional structures that regulate resource use may be understood and presented as sets of institutions and may be put into a relation. Correspondingly, the paper illustrates a qualitative comparative institutional analysis (QCIA) application procedure. It explains how QCA works, determines how it could be applied to CIA, and defines certain basic steps for QCIA application. The application of crisp-set and fuzzy-set QCA are presented step by step based on two examples – German agri-environmental payment schemes (AEM) and the Chinese Sloping Land Conversion Program (SLCP). Finally, challenges and benefits of QCA application to CIA of environmental governance structures are discussed. In sum, the paper shows that QCA may generally support the CIA of complex units, which are conducted by many institutional economists and institutionalists. QCA can help to facilitate the reduction of structural institutional complexity. Furthermore, QCA provides formalization for qualitative comparative aspects, and the generated results are highly policy relevant. However, there are certain challenges and limitations of QCIA that also cannot be neglected.