In an effort to analyze and solve evaluation of intrusion detection system, evaluation methods such as ROC curve, the Bayesian Detection Rate, the Expected Cost and the Intrusion Detection Capability had been established. The evaluation methods which only involved few evaluation metrics (such as false positive rate, false negative rate) had their own weaknesses, because the complexity of intrusion detection system is the main cause and evaluation of intrusion detection system must involve many performance indexes. In order to achieve the purpose of intrusion detection systems for comprehensive evaluation, this paper gives a method of entropy weight coefficient that is applied to calculate the weight of factors and decrease subjective judgment on the effect of the weight coefficient. Intrusion detection systems are evaluated objectively and comprehensively by the method of entropy weight coefficient.