In order to identify and attack the multi-UUV (unmanned underwater vehicle) groups, this paper proposes a method for identifying the critical nodes of multi-UUV formations. This method helps in combating multi-UUV formations by identifying the key nodes to attack them. Moreover, these multi-UUV formations are considered to have an unknown structure as the research object. Therefore, the network structure of the formation is reconstructed according to its space–time trajectory, and the importance of nodes is determined based on network structure entropy. As for the methodology, firstly, based on the swarm intelligence behavior method, the motion similarity of multi-UUV nodes in the formation is analyzed in pairs; furthermore, the leader–follower relationship and the network structure of the formation are calculated successively. Then, based on this network structure, the importance of the network nodes is further determined by the network structure entropy method. Finally, through simulation and experiments, it is verified that the algorithm can accurately construct the network structure of the unknown multi-UUV formation, and the accuracy of the calculated time delay data reaches 84.6%, and compared with the traditional information entropy algorithm, the ordering of the important nodes obtained by this algorithm is more in line with the underwater formation network.