Implementations for a space-optimized graph database system are provided. One implementation includes a computing system comprising: processing circuitry and memory storing instructions that causes the processing circuitry to: store a graph database comprising an initial tree graph storing a plurality of data entries, each data entry comprising a respective field identifier; receive a query to update the graph database, wherein the query comprises a request to add a new data entry; determine a splitting event to perform based on one or more predetermined criteria; generate a new tree graph corresponding to a field identifier of the new data entry by splitting off a subset of the plurality of data entries of the initial tree graph, wherein the subset comprises all data entries of the initial tree graph that correspond to the field identifier of the new data entry; and update the new tree graph in accordance with the query.