In order to deeply reveal the application characteristics of set pair analysis in structural water resources methodology and look forward to its main development trends, combined with existing research results, based on the methodological perspective of relational structure, a threeelement structural principle of structural water resources methodology system consisting of research object, research variable, and research objective (abbreviated as the Ternary Structure Principle) was summarized and proposed. Based on the principle, the application progress of ensemble analysis in modeling, optimization, identification, simulation, prediction, evaluation, decisionmaking, reasoning and other methods of structural water resources methodology was systematically expounded. It is pointed out that set pair analysis had obvious advantages in describing and handling the uncertain argumentation relationship between research variables and research objectives. The implementation process of the first seven methods reflects the information transmission between the research object, research variables, and research objectives, while the implementation process of the inference method reflects the information transmission between the evidence, argumentation, and conclusion relationship. Compared with the first seven methods, the abstraction and complexity level of the water resources system inference method are higher. The research approach of combining physical cause analysis of uncertainty formation process with quantitative calculation is an important development trend in the future to explore more systematic and pioneering water resource set pair analysis methods.