Various embodiments of the present disclosure generally relate to a memory system and an operating method thereof. According to the embodiments of the disclosed technology, the memory system may check first information indicating an execution state of a reference operation on each of the memory blocks during a preset target time period, may determine, based on the first information, at least one target memory block, among the plurality of memory blocks, as a target of a refresh operation of rewriting data stored in the target memory block and may execute a refresh operation on the target memory block.