With the rapid growth of big data, LSM-tree based key-value stores are widely applied due to its high efficiency in write performance. Compaction plays a critical role in LSM-tree, which merges old data and could significantly reduce the overall throughput of the whole system especially for write-intensive workloads. Hardware acceleration for database is a popular trend in recent years. In this paper, we design and implement an FPGA-based compaction engine to accelerate compaction in LSM-tree based key-value stores. To take full advantage of the pipeline mechanism on FPGA, the key-value separation and index-data block separation strategies are proposed. In order to improve the compaction performance, the bandwidth of FPGA-chip is fully utilized. In addition, the proposed acceleration engine is integrated with a classic LSM-tree based store without modifications on the original storage format. The experimental results demonstrate that the proposed FPGA-based compaction engine can achieve up to 92.0x acceleration ratio compared with CPU baseline, and achieve up to 6.4x improvement on the throughput of random writes.