Floods have been in a normalized way in recent years. The current Flood Control and Drought Relief Organization System has difficulty in coping with floods which become increasingly complicated. It is proposed that emergency management system of floods have to integrate bureaucracy with cooperative system, which corresponds with Chinese reality. Therefore, the management idea on bureaucracy-cooperation system is expounded. Then the organization structure of floods emergency management is constructed under the bureaucracy-cooperation system based on Crisis Management Shell Structure(CMSS). Finally, by taking Huaihu River Basin for example, the new organization structure under bureaucracy-cooperation system is designed, which contrasts with the current structure. It is then concluded that the former is more suitable to floods emergency management.