Organizational structure plays an important role in information transmission, consciousness enhancement, action control and effect feedback, and scientific design of organizational structure is an effective way to improve the headquarters' leadership. Based on this, the factors that influence the design of organizational structure are explored, including structural variables such as regularization, specialization and authority level,contingency factors such as organizational scale, objectives and strategies and external environment, and other outcome factors including efficiency and effect. In order to improve the leadership of headquarters,it is suggested to pay attention to the establishment of departments and post design, improve the level of specialization and regularization, and combine organizational design with organization construction to ensure that the enterprises headquarters can play the role of leadership and political core.