Model-based systems engineering (MBSE) provides an important capability for managing the complexities of system development. MBSE empowers the formalism of system architectures for supporting model-based requirement elicitation, specification, design, development, testing, fielding, etc. However, the modeling languages and techniques are heterogeneous, even within the same enterprise system, which leads to difficulties for data interoperability. The discrepancies among data structures and language syntaxes make information exchange among MBSE models more difficult, resulting in considerable information deviations when connecting data flows across the enterprise. Therefore, this article presents an ontology based upon graphs, objects, points, properties, roles, and relationships with extensions (GOPPRRE), providing metamodels that support the various MBSE formalisms across lifecycle stages. In particular, knowledge graph models are developed to support unified model representations to further implement ontological data integration based on GOPPRRE throughout the entire lifecycle. The applicability of the MBSE formalism is verified using quantitative and qualitative approaches. Moreover, the GOPPRRE ontologies are used to create the MBSE formalisms in a domain-specific modeling tool, MetaGraph, for evaluating its availability. The results demonstrate that the proposed ontology supports the formal structures and descriptive logic of the systems engineering lifecycle.