There exist various kinds of low level indices and uncertainty of evaluation information in the capability evaluation for air traffic control system. To solve this problem，a novel evaluation methodology using Dempster-Shafer(D-S) evidence reasoning is proposed. Firstly, the rule base is built with belief structure, and the input information is transformed into a pre-defined form. Then the activation weight of input is calculated. After that, the final assessment distribution is obtained by using evidence reasoning for index aggregation. The capability evaluation of a certain air traffic control system is investigated, so as to illustrate the feasiblity and effectiveness of the new methodology.