A method of operating a memory controller includes classifying a plurality of memory cells in an erase state into a plurality of groups, based on erase state information about the plurality of memory cells in the erase state; setting at least one target program state for at least some memory cells from among memory cells included in at least one of the plurality of groups; and programming the at least some memory cells for which the at least one target program state has been set, to a program state other than the at least one target program state from among the plurality of program states.