The index structure of comprehensive antiaircraft system is set up in this paper. And the paper applies fuzzy clustering and information entropy to synthetical evaluation. On the basis of the existing algorithm, it puts forward a new method based on fuzzy clustering and information entropy to evaluate antiaircraft system and then validates the method with examples. It proves that the method is correct and practical, so, the process of evaluation is in accord with people's cognition much better and the result of evaluation is more creditable.