There are provided a controller, a memory system having the same, and an operating method thereof. The controller includes a read counter configured to store a block read count value of a super block and memory blocks within a non-super block as a status information in an internal memory by counting a number of times that a read operation is performed on the memory blocks; and a super block manager configured to: store a super block reclaim trigger reference and a non-super block reclaim trigger reference, which is set for the super block and the non-super block, as the status information in the internal memory, divide data stored in the memory blocks into hot data and cold data according to the block read count value, and copy the hot data in the non-super block to the super block according to the status information.