Model-based systems engineering (MBSE) allows system models to formalize end-to-end systems engineering implementation while developing complex engineering system. The evolution of MBSE models, including changes and conflicts, provides important historical knowledge to support design decisions. Model versioning is an efficient approach to manage the evolution of MBSE models. However, the heterogeneous data structure and semantics used in MBSE practices hinder the tool interoperability that is required in model versioning, which also decreases the effectiveness and efficiency of system development. This paper proposes a tool-chain for model versioning of MBSE models based on a cognitive digital thread (CDT). In this tool-chain, the graph–object–point–property-relationship-role-extension (GOPPRR-E) modeling approach is adopted because it is compatible with heterogeneous modeling languages used in model versioning. To promote tool interoperability, this tool-chain adopts the Open Services for Lifecycle Collaboration to support conflict detection or resolution during model versioning. In particular, knowledge graphs are generated along with the model versioning workflow to develop a CDT, which provides the cognitive reasoning ability required for model versioning behaviors. A case study of landing gear system development is used to evaluate the feasibility of the proposed tool-chain through qualitative and quantitative analyses. The results demonstrate that the proposed tool-chain has better efficiency than traditional model versioning using Git tools.