Industrial information integration engineering (IIIE) is an interdisciplinary field to facilitate the industrial information integration process. In the age of complex and large-scale systems, model-based systems engineering (MBSE) is widely adopted in industry to support IIIE. Traceability management is considered the foundation of information management in MBSE. However, a lack of integration between stakeholders, development processes, and models can decrease the effectiveness and efficiency of the system development. A modified MBSE toolchain prototype has been developed to implement traceability management; however, a lack of formal and structured specifications makes it difficult to describe the complex topology in traceability management scenarios using this MBSE toolchain, such as creating traceability between heterogeneous models, which leads to poor reusability of this MBSE toolchain in other traceability management scenarios. To formalize traceability management scenarios using the MBSE toolchain, a cognitive thread (CT) ontology is developed in this study. The CT ontology is a specification expressing the information of stakeholders, models, and development processes for traceability management, providing the cognition capability to analyze the interrelationships between them. Based on the implementation of the modified MBSE toolchain, the concepts and interrelationships in the CT ontology are identified. The CT ontology is designed to develop the MBSE toolchain prototype for building, managing, and analyzing traceability in various traceability management scenarios. A case study of an adaptive cruise control system design is used to evaluate the completeness of the CT ontology through qualitative and quantitative analyses. The results demonstrate that the proposed CT ontology formalizes the information related to traceability management while using the proposed MBSE toolchain and can also be used in common traceability management scenarios to design other complex engineered systems.