Containers have been used in many applications for isolation purposes due to the lightweight, scalable and highly portable properties. However, to apply containers in virtual network functions (VNFs) faces a big challenge because high-performance VNFs often generate frequent communication workloads among containers while the container communications are generally not efficient. Compared with hardware modification solutions, properly distributing containers among hosts is an efficient and low-cost way to reduce communication overhead. However, we observe that this approach yields a trade-off between the communication overhead and the overall throughput of the cluster. In this paper, we focus on the communication-aware container re-distribution problem to optimize the communication overhead and the overall throughput jointly for VNF clusters. We propose a solution called FreeContainer which utilizes a novel two-stage algorithm to re-distribute containers among hosts. We implement FreeContainer in Baidu clusters with 6000 servers and 35 services deployed. Extensive experiments on real networks are conducted to evaluate the performance of the proposed approach. The results show that FreeContainer can increase the overall throughput up to 90% with significant reduction on communication overhead.