In sustainability science (SS), it is difficult to identify what needs to be solved, and it is also not clear how to solve the problems that are identified. There has been no consensus on the underlying question of ''What is structuring knowledge in SS?'' This paper focuses on knowledge structuring accompanied by supporting of thinking. It addresses the key challenges associated with knowledge structuring in SS, identifies the requirements for the structuring of knowledge, proposes a reference model, and develops an ontology-based mapping tool as a solution to one layer of the reference model. First, we identify the important requirements for SS knowledge structuring.Second, we develop a reference model composed of five layers based on three of the requirements. Third, we develop an ontology-based mapping tool at Layer 2 of the reference model for meeting the two major challenges for SS, namely, identifying what problems should be addressed in SS itself and proposing solutions for those problems. The tool is designed to store and retrieve information regarding SS, to provide access to a prototype ontology for SS, and to create multiple maps of conceptual chains depending on a user's interests and perspectives. Finally, we assess whether the developed tool successfully realizes the targeted part of the reference model for SS by examining the tool's conformity to the reference model, as well as its usability, effectiveness, and constraints. Although several issues were identified in the prototype ontology and the mapping tool, the study concluded that the mapping tool is useful enough to facilitate the function of Layer 2. In particular, the mapping tool can support thinking about SS from the viewpoint of: (a) finding new potentials and risks of technological countermeasures studied in SS; (b) helping users to get a more comprehensive picture of problems and their potential solutions; and (c) providing an effective opportunity to come up with new ideas that might not be thought of without such a tool.