With the quick development of network technology, the number of active IoT devices is growing rapidly. Numerous network scanning organizations have emerged to scan and detect network assets around the clock. This greatly facilitates illegal cyberattacks and adversely affects cybersecurity. Therefore, it is important to discover and identify network scanning organizations on the Internet. Motivated by this, we propose a network scanning organization discovery method based on a graph convolutional neural network, which can effectively cluster out network scanning organizations. First, we constructed a network scanning attribute graph to represent the topological relationship between network scanning behaviors and targets. Then, we extract the deep feature relationships in the attribute graph via graph convolutional neural network and perform clustering to get network scanning organizations. Finally, the effectiveness of the method proposed in this paper is experimentally verified with an accuracy of 83.41% for the identification of network scanning organizations.