The management interface of intellectual property rights(IPR)in water conservancy enterprises is complex, and the organizational structure and culture are the important organizational factors that cause their management interface conflicts. On the basis of defining the related concepts of the management interface of IPR of water conservancy enterprises, the manifestations of the management interface conflicts are summarized, and the influences of the organizational factors on the interface conflicts of IPR of water conservancy enterprises are analyzed from two aspects of organizational structure and culture. The corresponding countermeasures and suggestions are put forward.