Abstract: A novel method was proposed that using the design structure matrix (DSM) to optimize the topological sort in the business processes. And the rule of operation based on adjacency matrix method was designed. By comparing the proposed method with that of the traditional method, the limitation to the loop was overcome. Because the calculation were carried out from two sides at the same time, it was more effective than the old method. These explorations for the application of the DSM in the optimization of business processes are positive.