To improve the practicability and rationality of enterprise process structure optimization, an optimizing method based on directed hypergraph and resource constraint is presented. It models the resource-added process by a directed hypergraph. Based on the directed hypergraph theory and the process meaning added to the hypergraph, the process-structure-optimizing problem is transformed into the directed hypergraph cutting problem, and a set of formal optimizing rules of the process is given too. Then a process whose structure and supporting resource are optimized is obtained. Finally, an example is given to prove the feasibility and effectiveness of this method.