In this paper, a new model order reduction technique is presented by combining the benefits of the meta-heuristic cuckoo search optimization and Eigen permutation methods for order reduction of higher order continuous-time systems. In the proposed approach, the numerator and the denominator polynomials of reduced order model are determined by Cuckoo search and Eigen permutation approaches, respectively. The proposed approach preserves the stability of the original system into the lower order model as the Eigen permutationretains the dominant pole with simultaneous cluster formation of the remaining real and complex poles. The effectiveness of the proposed method is validated by single-input single-output and multiple-inputs multiple-outputs numerical examples.