This paper presents the use of graph databases in multi-domain modeling. Computational tools have been developed to model and analyze complex systems by querying system model elements and their relations across domains. Graph-based thinking is established as a tool in the research field of complexity management and product family design. The recent availability of general-purpose graph databases makes it possible to unify system model thinking and data storage. This paper connects graph databases with system modeling of multiple domains and presents an example of a product family structure. Data storage types as well as strengths and weaknesses of using graph databases in system modeling are presented.