Moving Target Defense (MTD) has emerged as a newcomer into the asymmetric field of attack and defense, and shuffling-based MTD has been regarded as one of the most effective ways to mitigate DDoS attacks. However, previous work does not acknowledge that frequent shuffles would significantly intensify the overhead. MTD requires a quantitative measure to compare the cost and effectiveness of available adaptations and explore the best trade-off between them. In this paper, therefore, we propose a new cost-effective shuffling method against DDoS attacks using MTD. By exploiting Multi-Objective Markov Decision Processes to model the interaction between the attacker and the defender, and designing a cost-effective shuffling algorithm, we study the best trade-off between the effectiveness and cost of shuffling in a given shuffling scenario. Finally, simulation and experimentation on an experimental software defined network (SDN) indicate that our approach imposes an acceptable shuffling overload and is effective in mitigating DDoS attacks.