In order to cope with the fast pace and high efficiency of cognitive electronic warfare, self-organizing competitive neural network is introduced to quickly evaluate the threat of cognitive electronic warfare to the communication system, so as to overcome the shortcomings of previous evaluation methods, such as poor evaluation effect and great dependence on prior knowledge. Firstly, the concept of cognitive electronic warfare and its threat to communication system are introduced. Secondly, by comparison, the self-organizing competitive neural network is selected as the core of communication threat evaluation. Finally, evaluation process is simulated by MATLAB simulation software to verify its effectiveness.