With the rapid development of artificial intelligence and enterprise digital transformation, the standardization organization, storage and management of semantic knowledge in computers have become the current research focus. As the core theory of knowledge system construction, knowledge organization (KO) provides theoretical support for the study of semantic knowledge organization and representation, among which knowledge organization system (KOS) is the important tool of semantic organization. At present, many scholars have carried out research from different perspectives of KOS based on theory, which provides the direction for the sustainable development of KOS. However, most of these studies focus on some aspects of KOS, which are in a "scattered" state, lacking systematic analysis of the basic principles of KOS construction and semantic organization based on theories and international standards. Therefore, this paper firstly constructs KOS theoretical models in the conceptual world and computer world respectively through a comprehensive study of multi-disciplinary basic theories such as semantics, logic, system theory, and international standards such as ISO 1087:2019, ISO 25964:2013, and ISO 11179:2023, and traces the iterative construction, organization and mapping process from "concept" in the conceptual world to "metadata" knowledge and semantics in the computer world. The semantic organization based on metadata is realized in computer. Secondly, on this basis, in order to realize ontology representation of domain knowledge, the ontology construction method based on MDR metadata is proposed. Finally, taking the semantic organization and ontology construction of Epicentre model in petroleum field as an example, the feasibility of the ideas and methods proposed in this paper is verified. The model and method proposed in this paper is independent of the specific type of KOS, so it is innovative and universal. The methodology is also applicable to other fields of conceptual system modeling, metadata standard construction, and data model modeling.