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The prevalence of 3D city models in urban applications is increasing due to their lightweight and flexibility, making them adaptable to various applications. However, effective data interoperability remains an issue. Managing 3D city models within a database can improve urban data management applications such as data enrichment and efficient querying. Motivated by the need for better interoperability of 3D city models, this paper proposes a novel method for storing CityJSON using the concept of a multi-model graph database as a foundation for enriching its semantics. The proposed approach involves decomposing CityJSON objects into smaller JSON components, which are then abstracted into graph elements. Parent-child and other relationship attributes are modelled to capture the hierarchical and associative structures of the CityJSON data. A specific programme is employed to preprocess CityJSON data based on several conditions before being loaded into the graph database. Our multi-model approach allows three types of queries: document, graph, and hybrid. The latter combines both document and graph query. Comparative evaluation against relational databases demonstrates that the proposed method outperforms in terms of query performance. The improved query performance is attributed to the advantage of graph database that reduces the need for joins and the ability to efficiently index and navigate JSON data. The findings of this study establish a foundation for semantic enrichment of 3D city models to improve interoperability and support advanced urban data management.