You would have to be more precise in describing what you mean by "all relationships between systems". A simple graph (meaning vertices and edges with no additional information) can encode the notions of a system and the existence of relationships between two systems, but without more structure you can't day much more. But this is already useful. If you have a big system you're trying to understand, a good first step is to draw a graph of the major components with edges indicating a dependency.

Systems interact through inputs and outputs, right? I mean, one system's output can be another system's input and even the second system's output can be the first one's input.

I guess my question was if there's something that can't be described or modelled with graphs.

As I said, my intuition is fuzzy, because I don't know much graph theory.