Embodiments of the present disclosure relate to a memory system and an operating method thereof. According to the embodiments of the present disclosure, the memory system may completely scan each of one or more target memory blocks among the plurality of memory blocks, once in each scan period to detect an error in data stored in the corresponding target memory block and may block an attempted second scan of each target memory block in a scan period in which the corresponding target memory block has already been scanned until the scan period is completed.