A memory system, a memory controller and an operating method are disclosed. By dividing a read count table including read count values respectively for a plurality of memory blocks into one or more read count table segments each including one or more read count values of a resolution, and managing one or more flags respectively corresponding to the read count table segments, and set the flag corresponding to the read count table segment in which at least one read count value is changed among the read count table segments, it is possible to minimize additional operational costs required to recover the read count table upon occurrence of an SPO.