Aimed at problems that there is a threat of emitter on timeliness, and complexity and imprecision exist in assessment process, a novel algorithm in assessment based on IFS-BN is proposed combined with Intuitionistic Fuzzy Sets (IFS) and Bayesian Network (BN). The IFS-BN algorithm fully describes determinacy, non-determinacy and hesitancy degree more adequately through the node information in Bayesian Network. On the basis of this, the algorithm substitutes priori probability calculated by Intuitional Fuzzy Sets into Bayesian Network model to obtain posteriori probability. Then, sequences of the threat level are acquired by posteriori probability. Meanwhile, corresponding evaluating index system of emitter threat assessment is established. The simulation shows that the algorithm is feasible and effective, and the results are much more objective and reasonable compared with the classical method of emitter threat assessment based on Bayesian Network.