A storage device generates and stores a key stream and a value stream by extracting from data a plurality of keys and a plurality of values respectively corresponding to the plurality of keys. The storage device includes a controller and a non-volatile memory. The controller receives from a host information about an invalid key included in the key stream together with a compaction command, and performs a compaction operation on the key stream in response to the compaction command. The non-volatile memory stores the key stream and the value stream. The controller merges the key stream with another key stream based on the information about the invalid key in the compaction operation.