Considering the deficiency of known operational efficiency evaluation of anti-missile operational efficiency evaluation, a new method based on distance measure and VIKOR is presented. The index system of weapon system anti-missile operational effectiveness evaluation is built, by the concept of intuitionistic fuzzy entropy, a good solution to the problem of evaluation under the attribute and decision maker weight unknown is obtained. On this basis, a comprehensive evaluation model of weapon system anti-missile operation based on distance measure and VIKOR, and ranking method of the assessment is given. Finally, via an example, the result of this evaluation technology is correct. The method proposed by this paper is valuable.