This paper was first based on the introduction of the fuzzy comprehensive evaluation method and the index system of innovation ability of industrial clusters, and apply the fuzzy comprehensive evaluation method to the cluster's innovation capability for the scientific evaluation, then do the practical situation on the Sichuan Cheng du software industry cluster, obtaining the result is consistent with the practical situation. Therefore, using the fuzzy analytic hierarchy process can not only be on different clusters for horizontal comparison analysis, but also on different periods of the same cluster of longitudinal analysis, so as to clear the superiority and the insufficiency of clusters in the innovation, this method are meaningful for the evaluation of cluster's innovation capability .