Branch threading in graph databases

The disclosed embodiments provide a system for processing queries of a graph database storing a graph, wherein the graph comprises a set of edges defined by a first linkage, a second linkage, and a third linkage. During operation, the system maintains the base version of an index of the graph database. Upon branching a version of the graph database from a first offset representing a virtual time in the base version of the graph database, the system creates a branched version of the index from a second offset corresponding to the virtual time in the base version of the index. The system then processes queries of the graph database based on the offsets and references from the branched version of the index to the base version of the index.