In order to solve the problems of existing threat assessment algorithms, a threat assessment method based on intuitionistic fuzzy three-way decision method is proposed. Firstly, the indexes are described by theory of intuitionistic fuzzy sets on the basis of that the threat assessment index system is established. Then, TOPSIS method is used to calculate the target threat. Finally, the targets are classified by three-way decision method according to the result of target threat. It is proved that it is feasible to introduce three-way decision method into threat assessment. At the same time, an improved algorithm for calculating the threshold of three-way decision is proposed. Experiments show that the improved algorithm has stable results and good classification effect.