The embodiments of the present disclosure relate to a memory system and operating method thereof. According to embodiments of the present disclosure, the memory system may include i) a memory device including a plurality of memory blocks each including a plurality of pages, and ii) a memory controller configured to monitor a program operation on a first super memory block among a plurality of super memory blocks each including at least one of the plurality of memory blocks, and execute a target operation on the first super memory block based on the state of the first super memory block when it is determined that the program operation on the first super memory block has not been executed for a preset time period from a preset reference time point.