A memory system includes: a memory device; a run-time bad block detector suitable for storing information of super memory blocks, each including a run-time bad block, in a bad list; a bit-map manager suitable for generating a bit-map representing integrity information of memory blocks in each of the super memory blocks; a short super block manager suitable for designating, among the super memory blocks, a super memory block having a number of run-time bad blocks less than or equal to a threshold as a short super memory block based on the bad list and the bit-map, whenever a logical unit configuration command is received from a host; and a processor suitable for controlling the memory device to simultaneously access normal blocks among the memory blocks forming the designated short super memory block and to perform a normal operation, based on the bit-map.